Composition for treatment of crigler-najjar syndrome

ABSTRACT

The invention provides a polynucleotide sequence (e.g., a gene, e.g., DNA or RNA) encoding UGT1A1 (e.g., expressing human UGT1A1). The invention further provides a vector, such as an adeno-associated virus (AAV) vector (e.g., AAV8) having a vector genome including inverted terminal repeat sequences and a UGT1A1 coding sequence operably linked to one or more expression control sequences (e.g., expression control sequences including a liver-specific promoter). Also provided are compositions containing these AAV vectors and methods of treating Crigler-Nijjar syndrome type I, Crigler-Nijjar syndrome type II, and Gilbert syndrome.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 16/061,945, filed Jun. 13, 2018, which is a National Stage Entry under US 35 U.S.C. 371 of International Patent Application No. PCT/US2016/066657, filed Dec.14, 2016, and which claims benefit under 35 U.S.C. 119(e) of U.S. Provisional Patent Application No. 62/348,029, filed Jun. 9, 2016, and U.S. Provisional Patent Application No. 62/266,969, filed Dec. 14, 2015. These applications are incorporated by reference herein.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED IN ELECTRONIC FORM

Applicant hereby incorporated by reference the Sequence Listing material filed in electronic form herewith. The file is labelled “16-7685US ST25.txt”.

BACKGROUND OF THE INVENTION

Crigler-Najjar (CN) syndrome is an autosomal recessive disorder of bilirubin metabolism that is caused by a variety of alterations in the coding sequence of the uridine diphosphate glucuronosyl transferase 1A1 (UGT1A1) gene. The total loss of UGT1A1 activity and the resulting severe jaundice and risk of neurological sequelae (kernicterus) are associated with CN type I. Although several drugs can slightly reduce jaundice, most current medical management relies on phototherapy for at least 12 hours per day. However, phototherapy rapidly becomes less effective following puberty, increasing the risk for kernicterus, and resulting in the need for liver transplantation to control the disease. Liver transplantation is not optimal, as it is risky for the patient and requires immune suppression. Additionally, since these patients sometimes require liver transplantation by the age of 10-13, multiple transplants may be required throughout the course of their lives.

Different animal models of the disease exist, including the natural occurring Gunn rat and a more recent knock-in mouse model of the diseases, which carries the same mutation present in the Gunn rat (Bortolussi et al., FASEB J., 2012, 26:1052-1062). Gunn rats present high bilirubin levels in serum and they have cerebellar hypoplasia; CN mice have a much more severe phenotype and die soon after birth if not promptly treated with phototherapy or gene therapy (Bortolussi et al., FASEB J., 2012, 26:1052-1062). Prior studies aimed at developing a gene-based therapy for CN showed that therapeutic efficacy could be achieved using adeno-associated virus (AAV) vectors delivered to the liver (Bortolussi et al, FASEB J. 2012, 26:1052-1062; Seppen et al., Molecular Therapy, 2006, 13(6):1085-1092). Botolussi et al, cited above, describe a study in a lethal mouse model of CN syndrome and reports that as low as 5 to 8% of normal liver expression and activity levels of UGT1A1 were sufficient to significantly reduce bilirubin levels and maintain lifelong low plasma bilirubin concentration.

CN type II is characterized by unconjugated hyperbilirubinemia due to reduced and inducible activity of hepatic bilirubin glucuronosyltransferase. Similarly, Gilbert syndrome is characterized by unconjugated hyperbilirubinemia caused by the reduced activity of glucuronyl transferase.

Therapies for treatment of CN syndrome type I and II, as well as Gilbert syndrome, and/or for delaying the earliest age of the subject in the absence of or in addition to the failure of liver transplantation are needed in the field.

SUMMARY OF THE INVENTION

The invention features a polynucleotide (e.g., a DNA or RNA molecule) encoding UGT1A1 (e.g., a UGT1A1 coding sequence, e.g., a polynucleotide that expresses human UGT1A1).

In another aspect, a vector (e.g., an adeno-associated virus (AAV) vector (e.g., an AAV8 vector)) is provided. In some embodiments, the AAV vector comprises a vector genome having AAV inverted terminal repeat sequences (ITRs) and a UGT1A1 coding sequence (e.g., a nucleic acid sequence comprising a UGT1A1 coding sequence). The UGT1A coding sequence can be operably linked to one or more expression control sequences (e.g., one or more expression control sequences comprising a liver-specific promoter). In some embodiments, the AAV vector (e.g., the AAV8 vector) has a vector genome having a heterologous secretion signal substituted for a native secretion signal. The vector genome may have multiple enhancers.

In one aspect, a UGT1A1 coding sequence useful in composition and methods for treating diseases associated with loss of UGT1A1 function, including, e.g., Crigler Najjar (CN) Syndrome I, CN II, and Gilbert syndrome, are provided. The sequences are selected from: (a) SEQ ID NO: 12; (b) SEQ ID NO: 14; (c) SEQ ID NO: 13; (d) SEQ ID NO: 4; (b) SEQ ID NO: 3; (c) SEQ ID NO: 2; or (d) SEQ ID NO: 1; its complementary strand, corresponding RNA, or a sequence 99% identical thereto which expresses human UGT1A1.

In another aspect, the invention provides a vector having a vector genome comprising a UGT1A1 coding sequence as identified herein operably linked to expression control sequences which direct transcription and/or expression of human UGT1A1. In certain embodiments, the vector is an adeno-associated virus (AAV). In still other embodiments, the vector has an AAV8 capsid. In certain embodiments, the expression control sequences comprise a liver-specific promoter.

In still other embodiments, a composition comprising a vector as described herein is provided in a formulation buffer. In a further aspect, a composition is provided which comprises an AAV vector of any of the preceding embodiments in a formulation buffer (e.g., a formulation buffer including phosphate buffered saline and a surfactant). In some cases, the AAV vector carries a gene encoding a human UGT1A protein and a pharmaceutically acceptable excipient, carrier, buffer, or preservative.

In another aspect, any of the preceding AAV vectors (e.g., AAV8 vectors) and/or compositions may be for use in treating a patient or patients having Crigler-Najjar (CN) syndrome (e.g., CN syndrome type I or CN syndrome type II) or Gilbert syndrome. In some cases, the patient is co-treated with an immunosuppressive and/or a phototherapy.

In certain embodiments, use of UGT1A1 coding sequence in treating Crigler-Najjar syndrome type I or II, or Gilbert syndrome with a UGT1A1 coding sequence described herein. In a further aspect, a composition is provided which comprises an AAV carrying a gene encoding a human UGT1A protein and a pharmaceutically acceptable excipient, carrier, buffer or preservative.

In still another aspect, a composition is provided which contains a rAAV vector as described herein for treatment of Crigler-Najjar syndrome type I or II, or Gilbert syndrome. Also described are methods of treatment Crigler-Najjar syndrome type I or II, or Gilbert syndrome. In certain embodiments, patient is co-treated with an immunosuppressive and/or phototherapy.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a quantification of Western blots for hUGT1A1 expression in liver homogenates from AAV-administered C57BL/6 mice. Male and female C57BL/6 mice were injected IV via the tail vein with 3×10¹² genome copies (GC)/kg of vectors expressing hUGT1A1 from a variety of vectors having different codons and different CpG less nucleotide sequences. At necropsy, livers were harvested and liver homogenates made. 1 μg of protein isolated from liver homogenate was run by Western blot with a human UGT1A1-specific antibody used for detection. Images of bands were quantified against the same amount of protein from a positive control sample. Values plotted as mean±SEM (n =5 mice/group). M, male; F, female; WPRE, denotes the first generation vector AAV 8. TBG.hUGT1A1co.WPRE.BGH.

FIG. 2 is a survival chart showing untreated UGT1 knock-out (KO) mice (none of which survived to day 7) and AAV-treated UGT1 knock-out mice following IV injection of test article into UGT1 KO mice within 24 hours of birth. Untreated UGT1 KO mice were observed daily from the time of birth. Mice either found dead or euthanized for clinical signs were genotyped. Treated UGT1 KO mice were injected IV with 10¹¹ GC/mouse of AAV8.TBG.hUGT1A1co.WPRE.BGH.

FIG. 3 shows serum total bilirubin levels in UGT1 KO following IV injection of AAV within 24 hours of birth and UGT1 KO mice following phototherapy. Total bilirubin levels in serum were measured at day 28 after birth. UGT1 KO mice were rescued to adulthood by either AAV treatment or phototherapy. AAV-treated UGT1 KO mice were injected IV with 10¹¹ GC/mouse of AAV8.TBG.hUGT1A1co.WPRE.BGH within 24 hours of birth (n=5). Phototherapy rescued UGT1 KO mice were exposed to phototherapy immediately after birth (blue florescent light, λ=450 nm; 10-30 μW/cm²/nm) for 12 hours per day for up to 21 days after birth (n=52). All mice were genotyped at weaning

FIGS. 4A-4B provide eGFP expression in C57BL/6J mice, Wistar rats, and NHP following IV injection of 10¹³ GC/kg of AAV8.TBG.eGFP.BGH. FIG. 4A. eGFP expression in the liver was quantified as percentage area transduction. FIG. 4B. DNA was extracted for quantification of GC. Values plotted as mean±SEM. ND, not determined.

FIGS. 5A-5B are line graphs showing reduction in serum total bilirubin levels in Gunn rats following IV injection of AAV8.TBG.hUGT1A1co.WPRE.BGH. Four week old female and male Gunn rats were injected IV with 3×10¹² GC/kg (triangle) or 3×10¹³ GC/kg (square) of AAV8.TBG.hUGT1Alco.WPRE.BGH or vehicle control (phosphate buffered saline (PBS)) (circle). Total bilirubin levels were measured in serum and percentage of baseline total bilirubin values calculated. Values are presented as mean±SEM.

FIGS. 6A-6B are bar charts showing hUGT1A1 mRNA transcript levels in liver from test or control article injected rhesus macaques. Rhesus macaques were injected IV with 1.0×10¹³ GC/kg and 2.5×10¹³ GC/kg of AAV8.TBG.U201mod.BGH (termed AAV8.TBG.hUGT1A1co in the figure) or control article (vehicle control). At necropsy, samples from the left, middle, and right lobes of the liver were harvested and snap frozen. RNA was extracted for quantification of vector transcript levels. FIG. 6A shows hUGT1A1 RNA copies presented per 100 ng of RNA. FIG. 6B shows Corrected relative expression of hUGT1A1 RNA levels. Values plotted as mean±SEM (n=3 liver samples/animal).

FIG. 7 shows total bilirubin levels in test or control article injected UGT1 KO mice. Male and female UGT1 KO mice were injected IV with 2.5×10¹⁰ GC/kg, 2.5×10¹¹ GC/kg, 2.5×10¹² GC/kg, and 2.5×10¹³ GC/kg of AAV8.TBG.U201mod.BGH (termed AAV8.TBG.hUGT1A1co in the figure) or control article (100 μl of vehicle control). Total bilirubin levels were measured in serum samples taken. Values expressed as mean±SEM.

FIG. 8 is a bar chart showing quantification of Western blots for hUGT1A1 expression in liver homogenates from test or control article injected UGT1 KO mice. Male and female UGT1 KO mice were injected IV with 2.5×10¹⁰ GC/kg, 2.5×10¹¹ GC/kg, 2.5×10¹² GC/kg, and 2.5×10¹³ GC/kg of AAV8.TBG.U201mod.BGH (termed AAV8.TBG.hUGTlAlco in the figure) or control article (100 μl of vehicle control). At necropsy, livers were harvested and liver homogenates made. 1μg of protein isolated from liver homogenate was run by Western blot with a human UGT1A1-specific antibody used for detection. Images of bands were quantified against the same amount of protein from a positive control sample. Values plotted as mean±SEM (n=5 mice/group). Bands for male mice injected with 2.5×10¹⁰ GC/kg were below the limit of detection.

FIGS. 9A-9B are bar charts showing hUGT1A1 mRNA transcript levels in liver from test or control article injected UGT1 KO mice. Male and female UGT1 KO mice were injected IV with 2.5×10¹⁰ GC/kg, 2.5×10¹¹ GC/kg, 2.5×10¹² GC/kg, and 2.5×10¹³ GC/kg of AAV8.TBG.U201DPmod.BGH (termed AAV8.TBG.hUGTlAlco in the figures) or control article (100 μl of vehicle control). At necropsy, livers were harvested and snap frozen. RNA was extracted for quantification of vector transcript levels. (A) hUGT1A1 RNA copies presented per 100 ng of RNA. (B) Corrected relative expression of hUGT1A1 RNA levels. Values plotted as mean±SEM (n=5 mice/group).

FIGS. 10A-10E provide an alignment of the novel UTG1A1 coding sequences provided herein: U201DP [SEQ ID NO: 3], U001 [SEQ ID NO: 1], U011TY [SEQ ID NO: 2], and UGT1A1co [SEQ ID NO: 4], with two published UGT1A1 sequence, termed v2.1 [SEQ ID NO: 7] and v3 [SEQ ID NO: 8].

DETAILED DESCRIPTION OF THE INVENTION

This invention relates to the use of a replication deficient adeno-associated virus (AAV) to deliver a UGT1A1 gene to liver cells of patients (human subjects) diagnosed with Crigler-Najjar (CN) syndrome I or II, or Gilbert syndrome. The recombinant AAV vector (rAAV) used for delivering the UGT1A1 gene (“rAAV.UGT1A1”) should have a tropism for the liver (e.g., an rAAV bearing an AAV8 capsid). The transgene may be controlled by liver-specific expression control elements. Such rAAV.UGT1A1 vectors can be administered by intravenous (IV) infusion to achieve therapeutic levels of UGT1A1 protein expression in the liver. Therapeutically effective doses of the rAAV.UGT1A1 range from greater than 2.5×10¹⁰ to 2.5×10¹³ genome copies (GC)/kg body weight of the patient, In one embodiment, the rAAV suspension has a potency such that a dose of at least 2.5×10¹¹ GC/kg administered to a mouse model of CN provided a reversal of total bilirubin levels to baseline levels. In another embodiment, the rAAV suspension has a potency such that a dose of at least 2.5×10¹² GC/kg administered to a human subject in need thereof provided a therapeutically effective lowering of total bilirubin levels. Optionally, the subjects are administered immunosuppressive agents in conjunction with therapy.

The terms “treat,” “treating,” and “treatment” refer to reducing the progression of some or all symptoms, reducing the severity of some or all symptoms, or to prevent or delay the onset of some or all symptoms.

The goal of the treatment is to functionally replace the patient's defective UGT1A1 via rAAV-based liver-directed gene therapy to treat this disease and improve response to current treatments. The invention is based, in part, on the development of therapeutic compositions and methods that allow for the safe delivery of efficacious doses; and improved manufacturing methods to meet the purification production requirement for efficacious dosing in human subjects.

Efficacy of the therapy may be assessed after treatment, e.g., post-dosing, using total bilirubin levels and/or serum bilirubin levels as a surrogate biomarker for human UGT1A1 transgene expression in the patient. For example, a decrease in the total bilirubin levels or serum bilirubin levels after the gene therapy treatment would indicate the successful transduction of functional UGT1A1. Patients who are candidates for treatment include neonates, infants, children and adults (male or female ≥18 years of age) diagnosed with CN Syndrome I or II. Prior to treatment, the patient may be assessed for neutralizing antibodies (NAb) to the AAV serotype used to deliver the UGT1A gene. Additionally, or alternatively, patients are monitored for elevated liver enzymes, which may be treated with transient immunosuppressant therapy (e.g., if at least about 2× baseline levels of aspartate transaminase (AST) or alanine transaminase (ALT) are observed).

As used herein, the term wild-type “UGT1A1” refers to the wild-type human UDP-glycosyltransferase 1 family 1, polypeptide A, (UGT1A1) cDNA shown in SEQ ID NO: 5 (accession number NM 000463.2, that is the reference sequence for the CDS of the mRNA for UGT1A1 human; OMIM reference 191740). The encoded enzyme is shown in SEQ ID NO: 6.

Provided herein are nucleic acid sequences encoding the UGT1A1 enzyme having sequences which are less than 95% identical to human wild-type sequence, SEQ ID NO:5. More particularly, sequences provided herein may be less than 90% identical, less than 85% identical, less than 80% identical, or as low as about 60% identical, or about 70% to 95% identical to the human wild-type sequence.

In one embodiment, the human UGT1A1 coding sequence is selected from U001 [SEQ ID NO: 1], U001mod [SEQ ID NO: 13], U011TY [SEQ ID NO: 2], U011TYmod [SEQ ID NO: 14], U201DP [SEQ ID NO: 3], U201DPmod [SEQ ID NO: 12], or the sequence of SEQ ID NO: 4. In certain embodiments, sequences having at least 99% identity to one of SEQ ID NO: 1-4, 12-14, these sequences may be used in a vector as described herein.

In certain embodiments, the engineered hUGT1A1 coding sequence selected for the vector genome is that of SEQ ID NO: 4. Suitably, this sequence has less than about 80% identity to wild-type human UGT1A1 gene [reproduced in SEQ ID NO:5], and less than about 95% identity or 90% identity, respectively to previously published engineered sequences. The sequence provided herein is particularly well suited for AAV8-mediated delivery and expression from the vector genome illustrated in the examples herein.

In certain embodiments, the UGT1A1 coding sequence is SEQ ID NO: 12. This sequence has about 99% identity to SEQ ID NO: 3. However, this sequence is less than about 85% identical to the wild-type human UGT1A1 gene [reproduced in SEQ ID NO:5], and less than about 95% identity, respectively to previously published engineered sequences. The sequence provided herein is particularly well suited for AAV8-mediated delivery and expression from the vector genome illustrated in the examples herein.

In certain embodiments, a vector genome as provided herein comprises AAV 5′ ITR, two enhancers, a promoter, an intron, a linker sequence, the CN coding sequence, a polyA, and an AAV 3′ ITR. In certain embodiments, the ITRs are from AAV2, which is a source different from the AAV capsid (e.g., AAV8). In certain embodiments, the two enhancers are two copies of the same enhancer, e.g., alpha mic/bik. In certain embodiments, the promoter is a liver-specific promoter (e.g., a TBG promoter). In certain embodiments, the vector genome further comprises a Kozak sequence. In certain embodiments, the polyA is a bovine growth hormone polyA. Illustrated vector genomes are provided herein as nt 1 to 3558 of SEQ ID NO: 9, nt 1 to 3153 of SEQ ID NO: 10, nt 1 to 3140 of SEQ ID NO: 15 [AAV.TBG.U201DPmod.BGH], nt 1 to 3140 of SEQ ID NO: 16 [AAV.TBG.U011TYmod.BGH], nt 1 to 3140 of SEQ ID NO: 17 [AAV.TBG.U001mod.BGH]. These sequence provided herein is particularly well suited for

AAV-mediated delivery, and in particularly, AAV8-mediated delivery. For example, AAV8-based vector, AAV8.TBG.U201DPmod.BGH is illustrated as the second-generation vector in the examples (i.e., AAV8.TBG.hUGT1Alco in figures/figure legends of FIGS. 6-9;) and the AAV8-based vector having the vector genome of nt 1-3153 of SEQ ID NO: 10 is illustrated in the studies shown in FIGS. 1-5.

As used herein, the term “NAb titer” refers to a measurement of how much neutralizing antibody (e.g., anti-AAV NAb) is produced which neutralizes the physiologic effect of its targeted epitope (e.g., an AAV). Anti-AAV NAb titers may be measured as described in, e.g., Calcedo, R., et al., Worldwide Epidemiology of Neutralizing Antibodies to Adeno-Associated Viruses. Journal of Infectious Diseases, 2009. 199(3): p. 381-390, which is incorporated by reference herein.

The terms “percent (%) identity”, “sequence identity”, “percent sequence identity”, or “percent identical” in the context of nucleic acid sequences refers to the bases in the two sequences which are the same when aligned for correspondence. The length of sequence identity comparison may be over the full-length of the genome, the full-length of a gene coding sequence, or a fragment of at least about 500 to 5000 nucleotides, or as desired. However, identity among smaller fragments, e.g. of at least about nine nucleotides, usually at least about 20 to 24 nucleotides, at least about 28 to 32 nucleotides, at least about 36 or more nucleotides, may also be desired. Multiple sequence alignment programs are also available for nucleic acid sequences. Examples of such programs include, “Clustal W”, “CAP Sequence Assembly”, “BLAST”, “MAP”, and “MEME”, which are accessible through Web Servers on the internet. Other sources for such programs are known to those of skill in the art. Alternatively, Vector NTI utilities are also used. There are also a number of algorithms known in the art that can be used to measure nucleotide sequence identity, including those contained in the programs described above. As another example, polynucleotide sequences can be compared using Fasta™, a program in GCG Version 6.1. FastaTM provides alignments and percent sequence identity of the regions of the best overlap between the query and search sequences. For instance, percent sequence identity between nucleic acid sequences can be determined using FastaTM with its default parameters (a word size of 6 and the NOPAM factor for the scoring matrix) as provided in GCG Version 6.1, herein incorporated by reference.

Percent identity may be readily determined for amino acid sequences over the full-length of a protein, polypeptide, about 32 amino acids, about 330 amino acids, or a peptide fragment thereof or the corresponding nucleic acid sequence coding sequencers. A suitable amino acid fragment may be at least about 8 amino acids in length, and may be up to about 700 amino acids. Generally, when referring to “identity”, “homology”, or “similarity” between two different sequences, “identity”, “homology” or “similarity” is determined in reference to “aligned” sequences. “Aligned” sequences or “alignments” refer to multiple nucleic acid sequences or protein (amino acids) sequences, often containing corrections for missing or additional bases or amino acids as compared to a reference sequence. Alignments are performed using any of a variety of publicly or commercially available Multiple Sequence Alignment Programs. Sequence alignment programs are available for amino acid sequences, e.g., the “Clustal X”, “MAP”, “PIMA”, “MSA”, “BLOCKMAKER”, “MEME”, and “Match-Box” programs. Generally, any of these programs are used at default settings, although one of skill in the art can alter these settings as needed. Alternatively, one of skill in the art can utilize another algorithm or computer program which provides at least the level of identity or alignment as that provided by the referenced algorithms and programs. See, e.g., J. D. Thomson et al, Nucl. Acids. Res., “A comprehensive comparison of multiple sequence alignments”, 27(13):2682-2690 (1999).

As used herein, a “functional fragment” refers to a portion of a referenced polynucleotide or a sequence having at least 95% (e.g., at least 99%) identity to the referenced sequence, which is sufficient to treat a UGT1A1-associated disease symptom in a human or a knockout mouse.

The expression cassette typically contains a promoter sequences as part of the expression control sequences. In one embodiment, a tissue-specific promoter is selected. As used herein, “a tissue-specific promoter” is a promoter which has activity in only a single type of tissue or a selected subset of cell types. This contrasts with constitutive promoters which direct expression in virtually all tissues and are largely, if not entirely, independent of environmental and developmental factors. Promoter activity can be evaluated by assessing transcription levels of the gene operably linked to the promoter as compared to at least one reference tissue (e.g., by detecting mRNA levels using PCR techniques) and/or by assessing expression levels of the gene product in the target tissue as compared to at least one reference tissue. Thus, one may be able to determine that a given promoter is tissue-specific by either its lack of activity in at least one reference tissue and/or by its activity in the selected tissue as compared to at least one reference tissue. A variety of assays are known in the art for assessing transcription and expression levels. Thus, for a “liver-specific promoter”, activity levels above an assay baseline may be detected in liver, whereas if assessed in another reference tissue, no activity is detected. Specificity may vary among promoters. There may be tissue-specific promoters which exhibit no detectable transcription or expression in other tissues, whereas some may exhibit higher transcription and/or expression levels in the target tissue (e.g., at least 10% to 100%, at least 25% higher, at least 30% higher, at least 50% higher, at least 75% higher, at least 80% higher, at least 90% higher, and amounts therebetween), as compared to at least one reference tissue. In certain embodiments, muscle may be selected as reference tissue for comparison to a suspected “liver-specific promoter” (e.g., TBG). In certain embodiments of the invention, a liver-specific promoter is selected. See, e.g., The Liver Specific Gene Promoter Database, Cold Spring Harbor. Liver specific promoters include, thyroxin binding globulin (TBG), alpha 1 anti-trypsin (A1AT); human albumin Miyatake et al., J. Virol., 71:5124 32 (1997), humAlb; and hepatitis B virus core promoter, Sandig et al., Gene Ther., 3:1002 9 (1996)f TTR minimal enhancer/promoter, alpha-antitrypsin promoter, and LSP (845 nt) 25 (requires intron-less scAAV), alcohol dehydrogenase 1, alcohol dehydrogenase 2, alcohol dehydrogenase 3, alcohol dehydrogenase 4, aldolase B, alpha fibrinogen, alpha-1-Microglobulin/bikunin (mic/bik) precursor, alpha-2-macroglobulin, alpha-2-urinary globulin, alpha-fetoprotein, angiotensinogen, antithrombin, antithrombin iii, apolipoprotein A-I, apolipoprotein A-II, apolipoprotein B, apolipoprotein C-III, apolipoprotein E, arginase, aromatic L-amino acid decarboxylase, beta fibrinogen, biliary glycoprotein. C-reactive protein, C4b-binding protein alpha-chain, carbamoylphosphate synthetase I, catechol-O-methyltransferase, complement component C6, cytochrome P450 2E1, erythropoietin, factor IX, factor VII, factor VIII, factor X, gamma fibrinogen, glucose-6-phosphatase, haptoglobin, hepatic lipase, insulin receptor, insulin-like growth factor binding protein I, insulin-like growth factor II, medium-chain acyl-CoA dehydrogenase, multidrug-resistance protein 2, protein C inhibitor, protein C, serum amyloid A, thyroxine-binding globulin, transferrin, and vitamin D binding protein. Alternatively, other promoters, such as viral promoters, constitutive promoters, regulatable promoters [see, e.g., WO 2011/126808 and WO 2013/04943], or a promoter responsive to physiologic cues may be used may be utilized in the vectors described herein.

In addition to a promoter, an expression cassette and/or a vector may contain other appropriate transcription initiation, termination, enhancer sequences, efficient RNA processing signals such as splicing and polyadenylation (polyA) signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance secretion of the encoded product. Examples of suitable polyA sequences include, e.g., SV40, bovine growth hormone (bGH), and TK polyA. Examples of suitable enhancers include, e.g., the alpha fetoprotein enhancer, the TTR minimal promoter/enhancer, LSP (TH-binding globulin promoter/alphal-microglobulin/bikunin enhancer), amongst others. In one embodiment, the expression cassette further contains a woodchuck hepatitis virus post-transcriptional regulatory element (WPRE). In other embodiments, the vectors contain no WPRE element. In still other embodiments, the vector has been modified to reduce CpG-sites.

In one embodiment, the expression cassette comprises an intron, e.g.,, an intron placed between the promoter and the coding sequence. An intron may be introduced to increase mRNA stability, 5′ capping, and the production of the protein. In a particular embodiment, the nucleic acid construct comprises a chimeric Promega intron. Other introns may include, e.g., human beta globin b2 (or HBB2) intron, a coagulation factor IX (FIX) intron, a SV40 intron or a chicken beta-globin intron.

These control sequences are “operably linked” to the UGT1A1 gene sequences. As used herein, the term “operably linked” refers to both expression control sequences that are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.

The expression cassette may be engineered onto a plasmid which is used for production of a viral vector. The minimal sequences required to package the expression cassette into an AAV viral particle are the AAV 5′ and 3′ inverted terminal repeats (ITRs), which may be of the same AAV origin as the capsid, or which of a different AAV origin (e.g., to produce an AAV pseudotype). In one embodiment, the ITR sequences from AAV2, or the deleted version thereof (AITR), are used for convenience and to accelerate regulatory approval. Alternatively, ITRs from other AAV sources may be selected. Where the source of the ITRs is from AAV2 and the AAV capsid is from another AAV source, the resulting vector may be termed pseudotyped. Typically, an expression cassette for an AAV vector comprises an AAV 5′ ITR, the UTG1A1 coding sequences and any regulatory sequences, and an AAV 3′ ITR. However, other configurations of these elements may be suitable. A shortened version of the 5′ ITR, termed AITR, has been described in which the D-sequence and terminal resolution site (trs) are deleted. In other embodiments, the full-length AAV 5′ and 3′ ITRs are used.

The abbreviation “sc” refers to self-complementary. “Self-complementary AAV” refers a plasmid or vector having an expression cassette in which a coding region carried by a recombinant AAV nucleic acid sequence has been designed to form an intra-molecular double-stranded DNA template. Upon infection, rather than waiting for cell mediated synthesis of the second strand, the two complementary halves of scAAV will associate to form one double stranded DNA (dsDNA) unit that is ready for immediate replication and transcription. See, e.g., D M McCarty et al, “Self-complementary recombinant adeno-associated virus (scAAV) vectors promote efficient transduction independently of DNA synthesis”, Gene Therapy, (August 2001), Vol 8, Number 16, Pages 1248-1254. Self-complementary AAVs are described in, e.g., U.S. Pat. Nos. 6,596,535; 7,125,717; and 7,456,683, each of which is incorporated herein by reference in its entirety.

The rAAV.hUGT1A1 vector should have a tropism for the liver (e.g., an rAAV bearing an AAV8 capsid). The vector can be formulated in a buffer/carrier suitable for infusion in human subjects. The buffer/carrier may include a component that prevents the rAAV, from sticking to the packaging or infusion tubing but does not interfere with the rAAV binding activity in vivo.

An AAV viral vector is an AAV nuclease-resistant particle having an AAV protein capsid into which are packaged nucleic acid sequences for delivery to target cells. An AAV capsid is composed of about 60 capsid protein subunits, VP1, VP2, and VP3, that are arranged in an icosahedral symmetry in a ratio of approximately 1:1:10 to 1:1:20, depending upon the selected AAV. AAV serotypes may be selected as sources for capsids of AAV viral vectors (DNase resistant viral particles) including, e.g., AAV1, AAV2, AAV3, AAV3B, AAV4, AAVS, AAV6, AAV6.2, AAV7, AAV8, AAV9, rh10, AAVrh64R1, AAVrh64R2, or rh8 (See, e.g., U.S. Publication Nos. 2007/0036760 and 2009-0197338, and EP 1310571). See also, International Publication No. WO 2003/042397 (AAV7 and other simian AAV), U.S. Pat. Nos. 7,790,449 and 7,282,199 (AAV8), International Publication No. WO 2005/033321, U.S. Pat. No. 7,906,111 (AAV9), and International Publication Nos. WO 2006/110689 and WO 2003/042397 (rh10). Other examples may include one or more variant VP capsid proteins (VP) such as those described in International Publication No. WO 2015/013313, e.g., the RHM4-1, RHM15-1, RHM15-2, RHM15-3/RHM15-5, RHM15-4 and RHM15-6 capsid variants, which are described as presenting a high liver tropism, and the documents cited therein. International Publication No. WO 2015/013313 refers to a “modified capsid” as a chimeric capsid or capsid comprising one or more variant VP capsid proteins derived from one or more wild-type AAV VP capsid proteins. In a particular embodiment, the AAV vector is a chimeric vector, i.e., its capsid comprises VP capsid proteins derived from at least two different AAV serotypes, or comprises at least one chimeric VP protein combining VP protein regions or domains derived from at least two AAV serotypes. The aforementioned documents also describe other AAV which may be selected for generating AAV, each of which are incorporated by reference. In some embodiments, an AAV cap for use in the viral vector can be generated by mutagenesis (e.g., by insertions, deletions, or substitutions) of one of the aforementioned AAV Caps or its encoding nucleic acid. In some embodiments, the AAV capsid is chimeric, comprising domains from two or three or four or more of the aforementioned AAV capsid proteins. In some embodiments, the AAV capsid is a mosaic of VP1, VP2, and VP3 monomers from two or three different AAVs or recombinant AAVs. In some embodiments, a rAAV composition comprises more than one of the aforementioned caps.

As used herein, “AAV8 capsid” refers to the AAV8 capsid having the encoded amino acid sequence of GenBank accession:YP 077180, which is incorporated by reference herein, and reproduced in SEQ ID NO: 11. Some variation from this encoded sequence is encompassed by the present invention, which may include sequences having about 99% identity to the referenced amino acid sequence in GenBank accession:YP_077180 (U.S. Pat. Nos. 7,282,199, 7,790,449, 8,319,480, 8,962,330, 8,962,332; e.g., less than about 1% variation from the referenced sequence). In another embodiment, the AAV8 capsid may have the VP1 sequence of the AAV8 variant described in International Publication No. WO 2014/124282, which is incorporated by reference herein. Methods of generating the capsid, coding sequences therefore, and methods for production of rAAV viral vectors have been described. (Gao et al., Proc. Natl. Acad. Sci. USA., 2003, 100(10), 6081-6086; U.S. Patent No. 2013/0045186; and International Publication No. WO 2014/124282).

For packaging an expression cassette into virions, the AAV inverted terminal repeat sequences (ITRs) are the only AAV components required in cis in the same construct as the gene expression cassette. Suitably, the coding sequences for the replication (rep) and/or capsid (cap) are removed from the AAV genome and supplied in trans or by a packaging cell line in order to generate the AAV vector. Thus, the vectors provided herein are replication-incompetent. A pseudotyped AAV may be provided which contains ITRs from a source which differs from the source of the AAV capsid. Additionally or alternatively, a chimeric AAV capsid may be utilized. Still other AAV components may be selected. Sources of such AAV sequences are described herein and may also be isolated or obtained from academic, commercial, or public sources (e.g., the American Type Culture Collection(ATCC®), Manassas, Va.). Alternatively, the AAV sequences may be obtained through synthetic or other suitable means by reference to published sequences such as are available in the literature or in databases such as, e.g., GenBank®, PubMed®, or the like.

Methods for generating and isolating AAV viral vectors suitable for delivery to a subject are known in the art. See, e.g., U.S. Pat. Nos. 7,790,449; 7,282,199; WO 2003/042397; WO 2005/033321, WO 2006/110689; and U.S. Pat. No. 7,588,772 B2]. In a one system, a producer cell line is transiently transfected with a construct that encodes the transgene flanked by ITRs and a construct(s) that encodes rep and cap. In a second system, a packaging cell line that stably supplies rep and cap is transiently transfected with a construct encoding the transgene flanked by ITRs. In each of these systems, AAV virions are produced in response to infection with helper adenovirus or herpesvirus, requiring the separation of the rAAVs from contaminating virus. More recently, systems have been developed that do not require infection with helper virus to recover the AAV—the required helper functions (i.e., adenovirus E1, E2a, VA, and E4 or herpesvirus ULS, ULB, UL52, and UL29, and herpesvirus polymerase) are also supplied, in trans, by the system. In these newer systems, the helper functions can be supplied by transient transfection of the cells with constructs that encode the required helper functions, or the cells can be engineered to stably contain genes encoding the helper functions, the expression of which can be controlled at the transcriptional or posttranscriptional level. In yet another system, the transgene flanked by ITRs and rep/cap genes are introduced into insect cells by infection with baculovirus-based vectors. For reviews on these production systems, see generally, e.g., Zhang et al., 2009, “Adenovirus-adeno-associated virus hybrid for large-scale recombinant adeno-associated virus production,” Human Gene Therapy 20:922-929, the contents of each of which is incorporated herein by reference in its entirety. Methods of making and using these and other AAV production systems are also described in the following U.S. patents, the contents of each of which is incorporated herein by reference in its entirety: U.S. Pat. Nos. 5,139,941; 5,741,683; 6,057,152; 6,204,059; 6,268,213; 6,491,907; 6,660,514; 6,951,753; 7,094,604; 7,172,893; 7,201,898; 7,229,823; and 7,439,065. See generally, e.g., Grieger & Samulski, 2005, “Adeno-associated virus as a gene therapy vector: Vector development, production and clinical applications,” Adv. Biochem. Engin/Biotechnol. 99: 119-145; Buning et al., 2008, “Recent developments in adeno-associated virus vector technology,” J. Gene Med. 10:717-733; and the references cited below, each of which is incorporated herein by reference in its entirety. The methods used to construct any embodiment of this invention are known to those with skill in nucleic acid manipulation and include genetic engineering, recombinant engineering, and synthetic techniques. See, e.g., Green and Sambrook et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (2012). Similarly, methods of generating rAAV virions are well known and the selection of a suitable method is not a limitation on the present invention. See, e.g., K. Fisher et al, (1993) J. Virol., 70:520-532 and U.S. Pat. No. 5,478,745.

The rAAV.hUGT1A1 vector can be manufactured as follows. Briefly, cells (e.g. HEK 293 cells) are propagated in a suitable cell culture system and transfected for vector generation. The rAAV.hUGT1A1 vector can then be harvested, concentrated and purified to prepare bulk vector which is then filled and finished in a downstream process.

Methods for manufacturing the gene therapy vectors described herein include methods well known in the art such as generation of plasmid DNA used for production of the gene therapy vectors, generation of the vectors, and purification of the vectors. In some embodiments, the gene therapy vector is an AAV vector and the plasmids generated are an AAV cis-plasmid encoding the AAV genome and the gene of interest, an AAV trans-plasmid containing AAV rep and cap genes, and an adenovirus helper plasmid. The vector generation process can include method steps such as initiation of cell culture, passage of cells, seeding of cells, transfection of cells with the plasmid DNA, post-transfection medium exchange to serum free medium, and the harvest of vector-containing cells and culture media. The harvested vector-containing cells and culture media are referred to herein as crude cell harvest.

The crude cell harvest may thereafter be subject method steps such as concentration of the vector harvest, diafiltration of the vector harvest, microfluidization of the vector harvest, nuclease digestion of the vector harvest, filtration of microfluidized intermediate, purification by chromatography, purification by ultracentrifugation, buffer exchange by tangential flow filtration, and formulation and filtration to prepare bulk vector.

In certain embodiments, methods similar to those described herein may be used in conjunction with other AAV producer cells. Numerous methods are known in the art for production of rAAV vectors, including transfection, stable cell line production, and infectious hybrid virus production systems which include Adenovirus-AAV hybrids, herpesvirus-AAV hybrids and baculovirus-AAV hybrids. See, e.g., G Ye, et al, Hu Gene Ther Clin Dev, 25: 212-217 (Dec 2014); R M Kotin, Hu Mol Genet, 2011, Vol. 20, Rev Issue 1, R2-R6; M. Mietzsch, et al, Hum Gene Therapy, 25: 212-222 (Mar 2014); T Virag et al, Hu Gene Therapy, 20: 807-817 (August 2009); N. Clement et al, Hum Gene Therapy, 20: 796-806 (August 2009); D L Thomas et al, Hum Gene Ther, 20: 861-870 (August 2009). rAAV production cultures for the production of rAAV virus particles all require; suitable host cells, including, for example, human-derived cell lines such as HeLa, A549, or 293 cells, or insect-derived cell lines such as SF-9, in the case of baculovirus production systems; 2) suitable helper virus function, provided by wild type or mutant adenovirus (such as temperature sensitive adenovirus), herpes virus, baculovirus, or a nucleic acid construct providing helper functions in trans or in cis; 3) functional AAV rep genes, functional cap genes and gene products; 4) a transgene (such as a therapeutic transgene) flanked by AAV ITR sequences; and 5) suitable media and media components to support rAAV production.

A variety of suitable cells and cell lines have been described for use in production of AAV. The cell itself may be selected from any biological organism, including prokaryotic (e.g., bacterial) cells, and eukaryotic cells, including, insect cells, yeast cells and mammalian cells. Particularly desirable host cells are selected from among any mammalian species, including, without limitation, cells such as A549, WEHI, 3T3, 10T1/2, BHK, MDCK, COS 1, COS 7, BSC 1, BSC 40, BMT 10, VERO, WI38, HeLa, a HEK 293 cell (which express functional adenoviral E1), Saos, C2C12, L cells, HT1080, HepG2 and primary fibroblast, hepatocyte and myoblast cells derived from mammals including human, monkey, mouse, rat, rabbit, and hamster. In certain embodiments, the cells are suspension-adapted cells. The selection of the mammalian species providing the cells is not a limitation of this invention; nor is the type of mammalian cell, i.e., fibroblast, hepatocyte, tumor cell, etc.

In order to ensure that empty capsids are removed from the dose of AAV. hUGT1A1 that is administered to patients, empty capsids are separated from vector particles during the vector purification process, e.g., using cesium chloride gradient ultracentrifugation. In one embodiment, the vector particles containing packaged genomes are purified from empty capsids using the process described in International Patent Application No. PCT/US16/65976, filed Dec. 9, 2016 and its priority documents U.S. patent application Ser. Nos. 62/322,098, filed Apr. 13, 2016 and U.S. patent application Ser. No. 62/266,341, filed on Dec. 11, 2015, and entitled “Scalable Purification Method for AAV8”, which is incorporated by reference herein. See, also, purification methods described in International Patent Application No. PCT/US16/65974, filed Dec. 9, 2016, and its priority documents, U.S. patent application Ser. Nos. 62/322,083, filed Apr. 13, 2016 and 62/266,351, filed Dec. 11, 2015 (AAV1); International Patent Appln No. PCT/US16/66013, filed Dec. 9, 2016 and its priority documents U.S. Provisional Applications No. 62/322,055, filed Apr. 13, 2016 and 62/266,347, filed Dec.11, 2015 (AAVrh10); and International Patent Application No. PCT/US16/65970, filed Dec. 9, 2016, and its priority applications U.S. Provisional Application Nos. 62/266,357 and 62/266,357 (AAV9), which are incorporated by reference herein. Briefly, a two-step purification scheme is described which selectively captures and isolates the genome-containing rAAV vector particles from the clarified, concentrated supernatant of a rAAV production cell culture. The process utilizes an affinity capture method performed at a high salt concentration followed by an anion exchange resin method performed at high pH to provide rAAV vector particles which are substantially free of rAAV intermediates.

In certain embodiments, the method separates recombinant AAV8 viral particles containing DNA comprising pharmacologically active genomic sequences from genome-deficient(empty) AAV8 capsid intermediates. The method involves (a) forming a loading suspension comprising: recombinant AAV8 viral particles and empty AAV8 capsid intermediates which have been purified to remove non-AAV materials from an AAV producer cell culture in which the particles and intermediates were generated; and a Buffer A comprising 20 mM Bis-Tris propane (BTP) and a pH of about 10.2; (b) loading the suspension of (a) onto a strong anion exchange resin, said resin being in a vessel having an inlet for flow of a suspension and/or solution and an outlet permitting flow of eluate from the vessel; (c) washing the loaded anion exchange resin with Buffer 1% B which comprises 10 mM NaCl and 20 mM BTP with a pH of about 10.2; (d) applying an increasing salt concentration gradient to the loaded and washed anion exchange resin, wherein the salt gradient ranges from 10 mM to about 190 mM NaCl, inclusive of the endpoints, or an equivalent; and (e) collecting the rAAV particles from eluate, said rAAV particles being purified away from intermediates.

In one embodiment, the pH used is from 10 to 10.4 (about 10.2) and the rAAV particles are at least about 50% to about 90% purified from AAV8 intermediates, or a pH of 10.2 and about 90% to about 99% purified from AAV8 intermediates. In one embodiment, this is determined by genome copies. A stock or preparation of rAAV8 particles (packaged genomes) is “substantially free” of AAV empty capsids (and other intermediates) when the rAAV8 particles in the stock are at least about 75% to about 100%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least 99% of the rAAV8 in the stock and “empty capsids” are less than about 1%, less than about 5%, less than about 10%, less than about 15% of the rAAV8 in the stock or preparation.

In one embodiment, the formulation is be characterized by an rAAV stock having a ratio of “empty” to “full” of 1 or less, preferably less than 0.75, more preferably, 0.5, preferably less than 0.3.

In a further embodiment, the average yield of rAAV particles is at least about 70%. This may be calculated by determining titer (genome copies) in the mixture loaded onto the column and the amount presence in the final elutions. Further, these may be determined based on q-PCR analysis and/or SDS-PAGE techniques such as those described herein or those which have been described in the art.

For example, to calculate empty and full particle content, VP3 band volumes for a selected sample (e.g., an iodixanol gradient-purified preparation where #of GC=# of particles) are plotted against GC particles loaded. The resulting linear equation (y=mx+c) is used to calculate the number of particles in the band volumes of the test article peaks. The number of particles (pt) per 20 μL loaded is then multiplied by 50 to give particles (pt)/mL. Pt/mL divided by GC/mL gives the ratio of particles to genome copies (pt/GC). Pt/mL-GC/mL gives empty pt/mL. Empty pt/mL divided by pt/mL and x 100 gives the percentage of empty particles.

Confirmation of the AAV/8 serotype of the vector may be achieved by an assay based upon analysis of peptides of the VP3 capsid protein by mass spectrometry (MS). The method involves multi-enzyme digestion (trypsin, chymotrypsin and endoproteinase Glu-C) of the VP3 protein band excised from SDS-PAGE gels followed by characterization on a UPLC-MS/MS on a Q-Exactive Orbitrap mass spectrometer to sequence the capsid protein. A tandem mass spectra (MS) method allows for identification of certain contaminant proteins and deriving peptide sequence from mass spectra.

Generally, methods for assaying for empty capsids and AAV vector particles with packaged genomes have been known in the art. See, e.g., Grimm et al., Gene Therapy (1999) 6:1322-1330; Sommer et al., Molec. Ther. (2003) 7:122-128. To test for denatured capsid, the methods include subjecting the treated AAV stock to SDS-polyacrylamide gel electrophoresis, consisting of any gel capable of separating the three capsid proteins, for example, a gradient gel containing 3-8% Tris-acetate in the buffer, then running the gel until sample material is separated, and blotting the gel onto nylon or nitrocellulose membranes, preferably nylon. Anti-AAV capsid antibodies are then used as the primary antibodies that bind to denatured capsid proteins, preferably an anti-AAV capsid monoclonal antibody, most preferably the B1 anti-AAV-2 monoclonal antibody (Wobus et al., J. Virol. (2000) 74:9281-9293). A secondary antibody is then used, one that binds to the primary antibody and contains a means for detecting binding with the primary antibody, more preferably an anti-IgG antibody containing a detection molecule covalently bound to it, most preferably a sheep anti-mouse IgG antibody covalently linked to horseradish peroxidase. A method for detecting binding is used to semi-quantitatively determine binding between the primary and secondary antibodies, preferably a detection method capable of detecting radioactive isotope emissions, electromagnetic radiation, or colorimetric changes, most preferably a chemiluminescence detection kit. For example, for SDS-PAGE, samples from column fractions can be taken and heated in SDS-PAGE loading buffer containing reducing agent (e.g., DTT), and capsid proteins were resolved on pre-cast gradient polyacylamide gels (e.g., Novex). Silver staining may be performed using SilverXpress (In vitrogen, CA) according to the manufacturer's instructions. In one embodiment, the concentration of AAV vector genomes (vg) in column fractions can be measured by quantitative real time PCR (Q-PCR). Samples are diluted and digested with DNase I (or another suitable nuclease) to remove exogenous DNA. After inactivation of the nuclease, the samples are further diluted and amplified using primers and a. TaqMan™ fluorogenic probe specific for the DNA sequence between the primers. The number of cycles required to reach a defined level of fluorescence (threshold cycle, Ct) is measured for each sample on an Applied Biosystems Prism 7700 Sequence Detection System. Plasmid DNA containing identical sequences to that contained in the AAV vector is employed to generate a standard curve in the Q-PCR reaction. The cycle threshold (Ct) values obtained from the samples are used to determine vector genome titer by normalizing it to the Ct value of the plasmid standard curve. End-point assays based on the digital PCR can also be used.

In one aspect, an optimized q-PCR method is provided herein which utilizes a broad spectrum serine protease, e.g., proteinase K (such as is commercially available from Qiagen). More particularly, the optimized qPCR genome titer assay is similar to a standard assay, except that after the DNase I digestion, samples are diluted with proteinase K buffer and treated with proteinase K followed by heat inactivation. Suitably samples are diluted with proteinase K buffer in an amount equal to the sample size, The proteinase K buffer may be concentrated to 2 fold or higher. Typically, proteinase K treatment is about 0.2 mg/mL, but may be varied from 0.1 mg/mL to about 1 mg/mL. The treatment step is generally conducted at about 55° C. for about 15 minutes, but may be performed at a lower temperature (e.g., about 37° C. to about 50° C.) over a longer time period (e.g., about 20 minutes to about 30 minutes), or a higher temperature (e.g., up to about 60° C.) for a shorter time period (e.g., about 5 to 10 minutes). Similarly, heat inactivation is generally at about 95° C. for about 15 minutes, but the temperature may be lowered (e.g., about 70 to about 90° C.) and the time extended (e.g., about 20 minutes to about 30 minutes). Samples are then diluted (e.g., 1000 fold) and subjected to TaqMan analysis as described in the standard assay.

Additionally, or alternatively, droplet digital PCR (ddPCR) may be used. For example, methods for determining single-stranded and self-complementary AAV vector genome titers by ddPCR have been described. See, e.g., M. Lock et al, Hu Gene Therapy Methods, Hum Gene Ther Methods. 2014 April; 25(2):115-25. doi: 10.1089/hgtb.2013.131. Epub 2014 Feb. 14.

The pharmaceutical compositions described herein are designed for delivery to subjects in need thereof by any suitable route or a combination of different routes. Direct delivery to the liver (optionally via intravenous, via the hepatic artery, or by transplant), oral, inhalation, intrathecal, intranasal, intratracheal, intraarterial, intraocular (e.g., intravitreal), intravenous, intramuscular, subcutaneous, intradermal, and other routes of administration.

The present invention also provides pharmaceutical compositions comprising a nucleic acid of the invention, or the vector of the invention, or the cell of the invention. Such compositions comprise a therapeutically effective amount of the UGT1A1. In certain embodiments, reaching expression levels as low as about 5% of wild-type expression levels can provide therapeutic benefit. In other embodiments, expression levels are higher than 5% of wild-type expression levels, e.g., more than 10%, more than 20%, more than 30%, or up to about 100% of wild-type expression levels.

The replication-defective viruses can be formulated with a physiologically acceptable carrier for use in gene transfer and gene therapy applications. In the case of AAV viral vectors, quantification of the genome copies (“GC”) may be used as the measure of the dose contained in the formulation. Any method known in the art can be used to determine the genome copy (GC) number of the replication-defective virus compositions of the invention. One method for performing AAV GC number titration is as follows: Purified AAV vector samples are first treated with DNase to eliminate un-encapsidated AAV genome DNA or contaminating plasmid DNA from the production process. The nuclease resistant particles are then subjected to heat treatment to release the genome from the capsid. The released genomes are then quantitated by real-time PCR using primer/probe sets targeting specific region of the viral genome (usually poly A signal). Another suitable method for determining genome copies are the quantitative-PCR (qPCR), particularly the optimized qPCR or digital droplet PCR [Lock Martin, et al, Human Gene Therapy Methods. April 2014, 25(2): 115-125. doi:10.1089/hgtb.2013.131, published online ahead of editing Dec.13, 2013].

The rAAV.UGT1A1 vector compositions can be formulated in dosage units to contain an amount of rAAV that is in the range of about 1.0×10⁹ GC to about 1.0×10¹⁴ GC (to treat an average adult subject of 70 kg in body weight), and preferably 1.0×10¹² GC to 1.0×10¹⁴ GC for a human patient. In another embodiment, the dose is less than about 1×10¹³ GC/kg. For example, the dose of AAV virus may be about 1×10⁹ GC, about 5×10⁹ GC, about 1 x 10¹⁰ GC, about 5×10¹⁰ GC, or about 2.5×10¹² GC. In another example, the variants may be delivered in an amount of about 0.001 mg to about 10 mg/kg.

The above-described recombinant vectors may be delivered to host cells according to published methods. The rAAV, preferably suspended in a physiologically acceptable carrier, may be administered to a human or non-human mammalian subject. The term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. or European Pharmacopeia or other generally recognized pharmacopeia for use in animals, and humans. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a preferred carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of suspensions, emulsions, sustained-release formulations and the like. Examples of suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin. In one embodiment, the vector is formulated in a composition comprising phosphate-buffered saline. In another particular embodiment, the vector is formulated in a composition comprising ringer lactate and a non-ionic surfactant, such as Pluronic® F68 at a final concentration of 0.01-0.0001%, such as at a concentration of 0.001%, by weight of the total composition. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to, ease pain at the, site of the injection.

The selection of the carrier is not a limitation of the present invention.

Optionally, the compositions of the invention may contain, in addition to the rAAV and carrier(s), other conventional pharmaceutical ingredients, such as preservatives, or chemical stabilizers. Suitable exemplary preservatives include chlorobutanol, potassium sorbate, sorbic acid, sulfur dioxide, propyl gallate, the parabens, ethyl vanillin, glycerin, phenol, and parachlorophenol. Suitable chemical stabilizers include gelatin and albumin.

A course of treatment may optionally involve repeat administration of the same viral vector (e.g., an AAV8 vector) or a different viral vector (e.g., an AAV8, an AAV3B, an AAVhu.37, and an AAVrh10). Still other combinations may be selected using the viral vectors described herein.

For example, treatment with an rAAV.UGT1A1 and compositions containing same may involve co-therapy with an immunosuppressive regimen. The immunosuppressive agent may be administered prior to the first vector administration, substantially simultaneously therewith, or may be administered after first vector administration. Optionally, the immunosuppressive regimen may be contained for 1 day-14 days, or shorter periods therebetween, e.g., 3 days, 7 days, 10 days, or for longer periods as needed or desired. Suitable immunosuppressive agents may be readily selected by one of skill in the art and may include, e.g., include, but are not limited to, steroids, antimetabolites, T-cell inhibitors, and alkylating agents. In certain embodiments, patients are monitored for elevated liver enzymes, and are optionally treated with transient immunosuppressant therapy (e.g., if at least about 2× baseline levels of aspartate transaminase (AST) or alanine transaminase (ALT) are observed).

Optionally, the composition described herein may be combined in a regimen involving other therapies, including, e.g., phototherapy.

Current phototherapy may involve exposure to therapeutic lamps (emission range: 400-525 nm, peak emission: 450-460 nm). Absent treatment as provided herein, patients undergo to phototherapy sessions for at least about 10 hours to about 12 hours/day, or longer. Patient's survival is dependent on the indefinite continuation of this therapy. Although initially very effective, phototherapy is inconvenient and the efficacy of this treatment is reduced with ageing due to increased thickness of skin and body surface/weight ratio; thus, patients are again at risk for kernicterus around time of puberty. To improve effectiveness of phototherapy it recommended to change lamps after about 1,000-1,500 hours of use (approximately every four to six months), keep the light source close to the body (about 15-20 centimeters, 6-8 inches), maximize skin exposure to light, use solid white sheets, and place reflective surfaces (mirrors and emergency blankets) around the bed.

In certain embodiments, a patient having Crigler-Najjar syndrome type I is treated with a combination of gene therapy and phototherapy. For example, phototherapy treatment may be initiated prior to treatment with gene therapy. Phototherapy may additionally or alternatively be administered for up to 24 hours to about 4 weeks, or points in-between (e.g., about 10 days, about 2 weeks, about three weeks) post-dosing with an AAV.UGT1A1 composition. Suitably, following about 4 weeks or less, post dosing with an AAV.UG1TA1 composition, the length of time required for phototherapy in a patient per day is reduced by at least about 30% to about 100%, or at least about 50%, at least about 75%, at least about 80%. In some embodiments, the patient may only require phototherapy on non-consecutive days. In another embodiment, phototherapy is no longer required in order to reduce bilirubin levels to acceptable levels.

In certain other embodiments, the patients are thereafter treated according to the conventional standard of care for Crigler-Najjar syndrome type II patients. In such patients, phenobarbital is used to control bilirubin levels and any CNS-related symptoms.

In certain embodiments, Crigler-Najjar syndrome type II patients may be treated with an AAV.hUGT1A1 composition as described herein. Phenobarbital or other therapy may additionally or alternatively be administered for 24 hours to about 4 weeks, or points in-between (e.g., about 10 days, about 2 weeks, about three weeks) post-dosing with an AAV.UGT1A1 composition. Suitably, following about 4 weeks or less, post dosing with an AAV.UGT1A1 composition, the dose of phenobarbital required in a patient per day is reduced by at least about 30% to about 100%, or at least about 50%, at least about 75%, at least about 80%. In another embodiment, phenobarbital is no longer required.

In certain embodiments, patients with defective UGT1A1 expression levels, Crigler-Najjar syndrome type I or II, who have been treated with AAAV.hUGT1A1 compositions as described herein, have elevated bilirubin levels such as found in patients having Gilbert's syndrome, but no further ongoing treatment is required.

It is to be noted that the term “a” or “an” refers to one or more. As such, the terms “a” (or “an”), “one or more,” and “at least one” are used interchangeably herein.

The words “comprise”, “comprises”, and “comprising” are to be interpreted inclusively rather than exclusively. The words “consist”, “consisting”, and its variants, are to be interpreted exclusively, rather than inclusively. While various embodiments in the specification are presented using “comprising” language, under other circumstances, a related embodiment is also intended to be interpreted and described using “consisting of” or “consisting essentially of” language.

As used herein, the term “about” means a variability of 10% from the reference given, unless otherwise specified.

The term “regulation” or variations thereof as used herein refers to the ability of a composition to inhibit one or more components of a biological pathway.

A “subject” is a mammal, e.g., a human, mouse, rat, guinea pig, dog, cat, horse, cow, pig, or non-human primate, such as a monkey, chimpanzee, baboon or gorilla.

As used herein, “disease”, “disorder” and “condition” are used interchangeably, to indicate an abnormal state in a subject.

The following examples are illustrative only and are not a limitation on the scope of the invention. A listing of abbreviations used herein is provided in Table 1, below

TABLE 1 List of abbreviations AAV Adeno-associated virus ACVP American College of Veterinary Pathologists ALP Alkaline Phosphatase ALT Alanine Aminotransferase AMC Animal Models Core ANOVA Analysis of variance APTT Activated partial prothrombin time AST Aspartate Aminotransferase BRB Biomedical Research Building CBC Complete blood count cDNA complementary Deoxyribonucleic Acid CFR Code of Federal Regulation CN Crigler-Najjar CPK Creatine phosphokinase CTL Cytotoxic T lymphocyte ddPCR Droplet digital polymerase chain reaction DPBS Dulbecco's phosphate buffered saline ELISA Enzyme-linked immunosorbent assay ELISPOT Enzyme-linked immunospot FDA Food and Drug Administration FDP Fibrin degradation products GC Genome copy GGT Gamma glutamyl transferase GLP Good Laboratory Practices GMP Good Manufacturing Practices GTP Gene Therapy Program H&E Hematoxylin and eosin stain hUGT1A1 Human UDP glucuronosyltransferase 1 family, polypeptide A1 IACUC Institutional Animal Care and Use Committee ID Identification IFN-γ Interferon-γ IM Intramuscular IV Intravenous kg Kilogram LFT Liver function test MED Minimal effective dose mg Milligram ml Milliliter NAb Neutralizing antibody NBF Neutral buffered formalin NHP Nonhuman primate NPRP Nonhuman Primate Research Program OCT Optimum cutting temperature OCTGT Office of Cellular, Tissue and Gene Therapies PBMC Peripheral blood mononuclear cell PT Prothrombin time QA Quality Assurance qPCR Quantitative PCR RT-qPCR Real time quantitative polymerase chain reaction SD Standard deviation SEM Standard error of the mean SOP Standard operating procedure SFU Spot forming unit TBG Thyroxine binding globulin TRL Translational Research Laboratories UDP Uridine phosphorylase UGT1A1 UDP glucuronosyltransferase 1 family, polypeptide A1 ULAR University Laboratory Animal Resources

Example 1 Vector Generation and Comparison

A series of vectors were constructed having five hUGT1A1 open reading frames (ORFs). See Table 2, below. In brief, there was no statistically significant difference in yield of the AAV8 vector lots for each of the five hUGT1A1 ORFs (Table 1).

When the HEK293 cells growing, the cells are transfected with each of three plasmids: the AAV serotype-specific packaging (trans) plasmid, the ad-helper plasmid, and vector cis plasmid containing the expression cassette for the UGT1A1 transgene flanked by AAV inverted terminal repeats (ITRs). Transfection is carried out using the calcium phosphate method. The full-length sequence of the cis plasmid carrying TBG.hUGT1A1co.WPRE.BGH is provided in SEQ ID NO: 9 (vector genome spanning from 5′ to 3′ ITR, nt 1-3558 of SEQ ID NO: 9). The full-length sequence of the cis plasmid carrying TBG.hUGT1A1co.BGH is provided in SEQ ID NO: 10 (vector genome spanning from 5′ to 3′ITR, nt 1-3152 of SEQ ID NO: 10). To construct the other plasmids, the coding sequences of SEQ ID NO:12 (UGT1A1 U201DP), SEQ ID NO: 13 (UGT1A1 U001), SEQ ID NO: 14 (UGT1A1 U011TY), or SEQ ID NO: 18 (U3G), is substituted for nt 1092-2690 of SEQ ID NO: 10. In other embodiments, a plasmid in which the ampicillin resistance gene is replaced by a kanamycin resistance gene is used. The trans plasmid used carries an AAV8 gene encoding the AAV8 capsid VP1 protein having the sequence of SEQ ID NO: 11. These vectors were evaluated in male and female wild type C57BL/6 mice following IV injection of 3×10¹² GC/kg of vector via the tail vein. Blood was taken by cardiac puncture at necropsy for evaluation of AST, ALT, alkaline phosphatase, and total bilirubin. Liver was harvested, with one lobe taken for fixation and paraffin embedding and the rest snap frozen and stored at −80° C. Expression was evaluated by hUGT1A1 protein levels determined by Western blot of liver homogenates with human UGT1A1-specific antibodies used for detection. Western blot images were quantified against the same amount of protein from a positive control sample.

TABLE 2 Yield of hUGT1A1 expressing vectors. Vector Name Total Yield (GC) AAV8.TBG.hUGT1A1co.WPRE.BGH 5.90 × 10¹³ AAV8.TBG.U001.BGH 1.29 × 10¹⁴ AAV8.TBG.U011TY.BGH 1.09 × 10¹⁴ AAV8.TBG.U201DP.BGH 5.95 × 10¹³ AAV8.TBG.U3G.BGH 1.31 × 10¹⁴

Liver samples were frozen on dry ice and stored at ≤−60° C. Tissue homogenates were made and Western blots to determine hUGT1A1 expression were performed as follows. Mouse liver samples were homogenized in RIPA Lysis and Extraction Buffer (ThermoFisher Scientific, Waltham, Mass., USA) and protease inhibitor using the QIAGEN TissueLyser II (QIAGEN, Hilden, Germany), in accordance with manufacturer's instructions. Protein levels were quantified by Pierce BCA Protein Assay Kit (ThermoFisher Scientific, Waltham, Mass., USA), in accordance with manufacture's instructions. Homogenates were diluted to enable 1 μg of protein to be run on the gel. Samples were heated at 95° C. for 5 minutes, separated on a NuPAGE Novex 10% Bis-Tris Protein Gels (ThermoFisher Scientific, Waltham, Mass., USA), and transferred to Trans-Blot Turbo PDVF membrane (BioRad, Hercules, Calif., USA). Membranes were blocked for one hour at room temperature in 5% non-fat milk, tris-buffered saline, 0.1% Tween 20 (TBS-T). Membranes were washed in 0.5% non-fat milk and TBS-T and then incubated with anti-UGT1A antibody (H-300 [sc-25847], Santa Cruz Biotechnology, Dallas, Tex., USA) overnight at 4° C. at an antibody dilution of 1:200 in 0.5% non-fat milk and TBS-T. Membranes were washed three times for five minutes each with TBS-T and then incubated with goat anti-rabbit HRP-conjugated antibody (sc-2054, Santa Cruz Biotechnology, Dallas, Tex., USA) for one hour at room temperature at an antibody dilution of 1:5000 in 0.5% non-fat milk and TBS-T. Membranes were washed three times for five minutes each with TBS-T and HRP was detected using Pierce ECL Western Blotting Substrate (ThermoFisher Scientific, Waltham, Mass., USA), in accordance with manufacturer's instructions. Images of bands were quantified against the same amount of protein from a positive control sample.

When assessed for protein expression, for two of the vectors (AAV8.TBG.U011TY.BGH and AAV8.TBG.U3G.BGH), the use of different codon optimized sequences significantly reduced expression compared to the AAV8.TBG.hUGT1A1co.WPRE.BGH vector. Expression of hUGT1A1 in female mice was reduced compared to that see in male mice. There were no significant differences in AST, ALT, alkaline phosphatase, and total bilirubin levels across the groups within a sex. Comparison of clinical chemistry values and hUGT1A1 expression by Western blot was performed using a one way analysis of variance with Tukey's multiple comparisons post-test within a sex.

Expression of hUGT1A1 was not significantly different between the AAV8.TBG.hUGT1A1co.WPRE.BGH vector and two of the second generation vectors (AAV8.TBG.U001.BGH, and AAV8.TBG.U201DP.BGH) in male mice (FIG. 1). Both of these second generation vectors lack the woodchuck post-regulatory element (WPRE) which has been previously described as enhancing transgene expression. However, there have been regulatory concerns raised regarding the safety of delivering WPRE to patients with a pre-existing liver disease. Since CN1 is a liver disease, vectors lacking this element are selected to proceed with further study.

Example 2 In Vivo Evaluation of the Efficacy of AAV8.TBG.hUGT1A1co.WPRE.bGH Following Systemic Administration in Newborn Pups

A. Summary

The purpose of this proof-of-concept (POC) study was to evaluate the initial vector designed for the treatment of CN, AAV8.TBG.hUGT1A1co.WPRE.BGH. This vector was administered to newborn UGT1 knockout (KO) mice to evaluate human UGT1A1 (hUGT1A1) expression and the ability of a gene therapy approach to increase survival of the UGT1 KO mouse model (an animal model of CN).

Three litters of mice (UGT1 KO: n=5; heterozygous: n=9; wild type [WT]: n=4) born following mating of heterozygous x heterozygous mice were injected intravenously (IV) with AAV8.TBG.hUGT1A1co.WPRE.BGH (10¹¹ genome copies [GC] per mouse) via the superficial temporal facial vein within 24 hours of birth. All mice were genotyped at weaning at day 21 post-birth. Blood samples were collected biweekly from day 28 post-birth throughout the in-life phase of the study for evaluation of serum total bilirubin levels. Mice were necropsied on day 270 post-test article administration. Liver was harvested at necropsy, fixed in 10% neutral buffered formalin, and processed for immunohistochemical staining for UGT1A1.

Neonatal gene therapy with AAV8.TBG.hUGT1A1co.WPRE.BGH protected UGT1 KO mice from lethal hyperbilirubinemia in the immediate postnatal period and significantly increased survival from 5 days in untreated UGT1 KO mice to 270 days post-test article administration (end of the study, p<0.0001 compared with untreated UGT1 KO mice). See FIG. 2. Rescued UGT1 KO mice appeared phenotypically identical to their heterozygous and WT littermates, albeit with elevated serum total bilirubin levels. Serum total bilirubin levels in the AAV-treated UGT1 KO mice were elevated by 5.7-fold compared with heterozygous and WT animals, but were reduced 15.2-fold when compared with UGT1 KO mice rescued to adulthood by phototherapy (p<0.0001 comparison by Student's t test). Dilution of the vector GCs in the liver due to proliferation of hepatocytes resulted in loss of some transgene expression and incomplete long term correction based on serum total bilirubin levels, which were elevated compared to heterozygous and WT littermates.

B. Methods

Mice were generated following heterozygous x heterozygous mating. All pups from three litters were administered with the test article within 24 hours of birth. Mice were ear tagged and genotyped at weaning, which occurred at 21 days post-birth.

The intravenous (IV) route via the superficial temporal facial vein was selected for use because it is the most efficient route used to target the liver, which in humans is the clinical site of the disease.

Efficacy of the test article was determined by total bilirubin levels in serum. In addition, immunohistochemical (IHC) analysis was performed to determine the levels of hUGT1A1 protein expression in the liver.

Changes in the serum total bilirubin levels of the animals were analyzed. Mice were anesthetized and blood collected by retro-orbital or submandibular technique during the in-life phase of the study or by cardiac puncture at necropsy. Blood was collected in labeled serum gel separator brown top tubes, allowed to clot, and then serum was isolated.

Comparison of survival curves was performed using a log-rank (Mantel-Cox) test. For serum total bilirubin data, cohort average and standard error of the mean (SEM) was calculated and reported. Student's t test was performed on the serum total bilirubin level data to determine any test article-related effects compared to mice rescued to adulthood by phototherapy.

C. Results

No mice died during the course of the study. Neonatal gene therapy with 10¹¹ genome copies (GC)/mouse AAV8.TBG.hUGT1Alco.WPRE.BGH protected UGT1 KO mice from lethal hyperbilirubinemia in the immediate postnatal period, with a significant increase in survival from 5 days in untreated UGT1 KO mice to 270 days in vector-treated mice (FIG. 2, p<0.0001 comparison of survival curves by log-rank (Mantel-Cox) test).

Mice were weighed from day 28 post-birth throughout the initial in-life phase of the study. All animals continued to gain weight over the course of the study. Rescued UGT1 KO mice appear phenotypically identical to their WT and heterozygous littermates and with no difference in body weight.

Serum total bilirubin levels were analyzed from day 28 post-birth throughout the in-life phase of the study. Serum total bilirubin levels in the AAV-treated UGT1 KO mice were elevated by 5.7-fold compared with heterozygous and WT animals, but were significantly reduced 15.2-fold compared with UGT1 KO mice rescued to adulthood by phototherapy (p<0.0001 comparison by Student's t test). Dilution of the vector GCs in the liver due to proliferation of hepatocytes results in loss of some transgene expression and incomplete long term correction based on total bilirubin levels, which are elevated compared to heterozygous and WT littermates. Therefore, neonatal gene therapy protected UGT1 KO mice from lethal hyperbilirubinemia in the immediate postnatal period and significantly increased survival. Rescued UGT1 KO mice appear phenotypically identical to their heterozygous and WT littermates, albeit with elevated total bilirubin levels.

UGT1 KO mice administered with test article as neonates were necropsied on day 270 post-vector administration and liver collected, fixed in 10% NBF, and processed for IHC staining for UGT1A1. Staining indicates hepatocytes expressing UGT1A1, which was sustained throughout the life of the mouse.

D. Conclusions

Neonatal gene therapy with AAV8.TBG.hUGT1A1co.WPRE.BGH protected UGT1 KO mice from lethal hyperbilirubinemia in the immediate postnatal period and significantly increased survival from 5 days in untreated UGT1 KO mice to 270 days post-test article administration (p<0.0001 compared with untreated UGT1 KO mice). Rescued UGT1 KO mice appeared phenotypically identical to their heterozygous and WT littermates, albeit with elevated total bilirubin levels. Serum total bilirubin levels in the AAV-treated UGT1 KO mice were elevated by 5.7-fold compared with heterozygous and WT animals, but were reduced 15.2-fold when compared with UGT1 KO mice rescued to adulthood by phototherapy (p<0.0001 comparison by Student's t test). Dilution of the vector GCs in the liver due to proliferation of hepatocytes resulted in loss of some transgene expression and incomplete long term correction based on serum total bilirubin levels, which were elevated compared to heterozygous and WT littermates.

Example 3 Phototherapy Study

A. Summary

The purpose of this proof-of-concept (POC) study was to evaluate the efficacy of phototherapy in UGT1 knockout (KO) mice, in an attempt to model the current treatment strategy for CN. Phototherapy has been previously reported to allow survival of UGT1 KO mice to adulthood by protecting affected mice from lethal hyperbilirubinemia in the immediate postnatal period.

Litters of mice born following heterozygous x heterozygous mating were exposed to blue florescent light (λ=450 nm; 10-30 μW/cm²/nm) for 12 hours per day for up to 21 days post-birth. At the time of weaning (day 21 post-birth), all offspring were genotyped.

While this study is currently ongoing as of this writing, 63 UGT1 KO mice have been weaned following phototherapy. These animals did not require to be maintained on phototherapy post-weaning and the majority of the mice demonstrate normal duration of survival. The UGT1 KO mice rescued by phototherapy had significantly elevated total bilirubin levels compared with the UGT1 KO mice that received AAV gene therapy (p<0.0001 comparison by Student's t test).

In the UGT1 KO mouse model, phototherapy in the immediate postnatal period protects the animals from kernicterus; after 3-4 weeks phototherapy can be withdrawn and the animals survive but with persistent hyperbilirubinemia. Pretreatment with phototherapy allows gene therapy vector administration to be delayed until the liver stops proliferating, which would simulate the likely clinical scenario.

B. Materials and Methods

Mice were generated following heterozgous x heterozgous mating. All pups born were exposed to the test article from birth. At weaning (day 21 after birth), mice were eartagged, genotyped, and removed from exposure to the test article.

Dose Necropsy Number of Number of Genotype (μW/cm²/nm) Time Point Males Females UGT1 KO 10-30 N/A 39 24

All pups born following mating of heterozygous x heterozygous mice were exposed to blue fluorescent light (λ=450 nm; 10-30 μW/cm²/nm) for 12 hours per day for up to 21 days after birth.

Efficacy of the test article was determined by survival. UGT1 KO mice die without treatment within 5 days of birth due to lethal hyperbilirubinemia in the immediate postnatal period.

Changes in the serum total bilirubin levels of the animals were analyzed by the contract facility Antech Diagnostics, Inc. Mice were anesthetized and blood collected by submandibular technique during the in-life phase of the study or by cardiac puncture at necropsy. Blood was collected in labeled serum gel separator brown top tubes, allowed to clot, and then serum was isolated.

Student's t test was performed on the serum total bilirubin level data to determine any test article-related effects compared to mice rescued to adulthood by phototherapy.

C. Results

See, FIG. 3. In the UGT1 KO mouse model, phototherapy in the immediate postnatal period protects the animals from kernicterus; after 3 to 4 weeks, phototherapy can be withdrawn and the animals survive but with persistent hyperbilirubinemia. Pretreatment with phototherapy before gene therapy allows vector administration to be delayed until the liver stops proliferating, which would simulate the likely clinical scenario.

Example 4 Efficacy of hUGT1A1 Following Systemic Administration of the Vector in the UGT1 KO Mouse Model

For the efficacy study, newborn pups are exposed to blue florescent light for 12 hours per day for up to 14 days post-birth. At the time of weaning, all offspring are genotyped and only UGT1−/− (knockout) animals are enrolled in the study.

Male and female UGT1 KO mice (6-12 weeks old) are administered the recombinant vector by IV injection at one of four doses increasing in full log units from 5×10¹⁰ GC/kg to 5×10¹³ GC/kg (equivalent to 10⁹ to 10¹² GC/mouse). Mice are necropsied on day 28 and day 90 post-vector administration with seven male and seven female mice per cohort. Cohorts of mice receiving vehicle only (phosphate-buffered saline [PBS]) are included as a vehicle control. Therefore, a total of 140 mice are used for this study.

After vector administration, the animals are monitored daily for general observations. Regular phlebotomies are performed post-vector administration and the collected serum is evaluated for total, direct, and indirect bilirubin levels. In addition, serum albumin, ALT, and AST levels is also evaluated. At the time of sacrifice, blood is collected for complete blood counts (CBC) and clinical chemistries, in addition to total, direct, and indirect bilirubin levels. A full necropsy is performed on seven animals (if no unexpected deaths) per group per time point with a thorough and systematic examination and dissection of the animal viscera and carcass. Tissues are collected at necropsy for vector biodistribution and transcript expression levels by qPCR and RT-qPCR, respectively. DNA and RNA is extracted from mice that received the highest vector dose and mice that received the vehicle control.

Example 5 Non-Clinical Pharmacology/Toxicology Study

The naturally occurring model of CN1, the Gunn rat, is on a Wistar background. Previous studies using AAV gene therapy in the Gunn rat would suggest that AAV8 transduces the liver less efficiently in this model, with AAV1 producing higher transduction levels (Seppen et al., Mol Ther, 13, 1085-92 (2006)). Prior to evaluation of our gene therapy product in the rat disease model, an AAV vector transduction comparison study in the wild type Wistar rat was performed. This study was also performed in wild type C57BL/6 mice as these are the background strain for the UGT1 KO mice.

In brief, for this pharmacology/toxicology study, male and female C57BL/6J mice (6-8 weeks old, weighing 20-28 g) are administered the following vector: AAV8.TGB.U201DPmod.BGH (an AAV8 capsid having packaged therein vector genome of SEQ ID NO: 15, generated using triple transfection techniques in 293 cells. This clinical candidate vector is administered by IV injection at one of three doses increasing in full or half log units from 5×10¹¹ GC/kg to 5×10¹³ GC/kg (equivalent to 10¹⁰ to 10¹² GC/mouse). Cohorts of mice receiving vehicle only (phosphate-buffered saline [PBS]) are included as a vehicle control. Mice are necropsied on days 3, 14, 90, and 180 with seven male and seven female mice per cohort. Therefore, a total of 224 mice are used for this study.

-   -   After vector administration, the animals are monitored daily for         general observations. At the time of sacrifice, blood is         collected for CBC and clinical chemistries. Evaluation of the         presence of inflammatory cytokines by multiplex ELISA assay         (Luminex) is performed on samples from mice necropsied at day 3         and compared to baseline levels. Splenocytes are isolated from         mice necropsied on day 14 post-vector administration to evaluate         cytotoxic T lymphocyte (CTL) responses. IFN-γ ELISPOT is         performed to evaluate the presence of AAV8 capsid- and         hUGT1A1-specific T cells. AAV8 neutralizing antibody (NAb)         titers is determined at day 28 post-vector administration.

A full necropsy is performed on seven animals (if no unexpected deaths) per group per time point with a thorough and systematic examination and dissection of the animal viscera and carcass. Tissues are collected at necropsy for gross pathology and histopathology examinations, vector biodistribution, and transcript expression levels. DNA and RNA are extracted from mice that received the highest vector dose and mice that received the vehicle control.

A. Summary

Male and female Wistar rats and male and female C57BL/6 mice (all 6-8 weeks old) were administered with two doses of AAV1, AAV5, and AAV8 vectors expressing enhanced green fluorescent protein (eGFP) by IV injection via the tail vein (10¹² GC/kg and 10¹³ GC/kg). The transduction efficiency of vectors was compared by evaluation of eGFP expression in the liver on day 7 post-vector administration. Based on initial results the study was expanded to include two further groups of male and female Wistar rats. These groups received either the AAV8.TBG.eGFP vector at a higher dose of 10¹⁴ GC/kg and were necropsied on day 7 post-vector administered or received a dose of 10¹³ GC/kg and were necropsied on day 14 post-vector administration.

In the Wistar rats, no differences in transduction efficiency were seen across the AAV capsids following IV administration of the same dose of vector. In male C57BL/6J mice (Jackson Laboratories), AAV8 transduction efficiency in the liver was seen in 97% of hepatocytes with extremely high transgene expression at a dose of 10¹³ GC/kg. In contrast, at the same vector dose, transduction efficiency in the Wistar rats with AAV8 was substantially reduced. Also, the efficiency of gene transfer into the rat liver by AAV8 was substantially lower compared with that in mice. Specifically, male mice had an average of 30.6 GC of the vector per diploid genome and male Wistar rats had an average of 1.7 GC of the vector per diploid genome detected in the liver.

Therefore, due to decreased transduction and gene transfer efficiencies in the rat relative to mice, further studies in this species would lead to a gross underestimation of the minimally effective dose for CN gene therapy applications. However, as rats were still receptive to some small level of AAV8 gene therapy the CN rat disease model, the Gunn rat, can still be used to provide additional evidence that the clinical candidate is functional. Furthermore, the Gunn rat would be useful to establish the relationship between transduction and efficacy.

B. Materials and Methods

Test Articles: AAV1.TBG.eGFP.BGH

-   -   AAV5.TBG.eGFP.BGH     -   AAV8.TBG.eGFP.BGH

Control Article: Phosphate Buffered Saline (PBS)

Efficacy of the test article was determined by enhanced green fluorescent protein (eGFP) expression in the liver. eGFP expression can be both visualized and images quantified as percent area expressing eGFP. Tissues were processed as described previously to visualize eGFP expression (Wang et al., Mol Ther, 18, 126-34 (2010), Wang et al., Hum Gene Ther, 22, 1389-401 (2011). Images were taken and eGFP expression in liver was quantified as the percentage of area expressing eGFP as described previously (Wang et al., 2010, Wang et al., 2011). Tissues samples were snap frozen at the time of necropsy and DNA was extracted using the QlAamp DNA Mini Kit (Qiagen, Valencia, CA, USA). Detection and quantification of vector GC in extracted DNA were performed by real-time PCR as described previously (Bell et al., Mol Ther, 14, 34-44 (2006). Briefly, genomic DNA was isolated and vector GCs were quantified using primers/probe designed against the BGH polyA sequence of the vector.

C. Results

eGFP Expression in Liver: In the Wistar rats, no differences in transduction efficiency were seen across the AAV capsids following IV administration of the same dose in animals necropsied on day 7 post-vector administration. Vector transduction levels across the three capsids evaluated were very low with only a few eGFP hepatocytes seen per field. Increasing the dose of the AAV8 vector to 10¹⁴ genome copies (GC)/kg or increasing the duration of the study to day 14 post-vector administration did increase transduction but overall the levels remained low. In C57BL/6J mice the transduction efficiency was substantially increased compared to that seen in the Wistar rats across the three vector capsids evaluated.

Quantification of eGFP Expression and Gene Transfer: The percentage area transduction and the vector genome copies in the liver for animals administered with AAV8 were determined (FIG. 4A-4B). In male C57BL/6J mice, AAV8 transduction efficiency in the liver was seen in 97% of hepatocytes with extremely high transgene expression at a dose of 10¹³ GC/kg (FIG. 4A). At the same vector dose, transduction efficiency in the Wistar rats with AAV8 was significantly reduced (FIG. 4B). For comparison , FIG. 4A also includes an image from our previously published work in rhesus macaques at 7 days post-vector administration, which showed vastly elevated transduction efficiency compared to rats (Wang et al, 2010, cited above) and determine the reason for the low transduction efficiency in rats, DNA was extracted from the harvested livers and vector GC quantified by qPCR. Interestingly gene transfer into the rat liver by AAV8 was also significantly reduced compared to mice, where male mice have an average of 30.6 GC per diploid genome and male Wistar rats have an average of only 1.7 GC per diploid genome being detected in the liver (FIG. 4B). From our previously published work in NHPs at day 7 there was an average of 23.2 GC per diploid genome present in the liver.

4. Conclusions

Due to decreased transduction and gene transfer efficiencies in the rat, it is likely that further studies in this species would lead to a gross underestimation of the minimally effective dose for CN gene therapy applications. However, as rats were still receptive to some small level of AAV8 gene therapy the CN rat disease model, the Gunn rat, can still be used to provide additional evidence that the clinical candidate is functional. Furthermore, the Gunn rat would be useful to establish the relationship between transduction and efficacy.

For comparison, our previously published work in rhesus macaques at 7 days post-vector administration showed vastly elevated transduction efficiency compared to rats, with 23.2 GC per diploid genome present in the liver.

Example 6 Evaluation of Vector Administration in the Gunn Rat

A. Summary

The purpose of this proof-of-concept (POC) study was to evaluate the initial vector designed for the treatment of Crigler-Najjar syndrome (CN), AAV8.TBG.hUGT1A1co.WPRE.BGH. This vector was administered to Gunn rats to evaluate human UGT1A1 (hUGT1A1) expression and the ability of a gene therapy approach to decrease total bilirubin levels. The Gunn rat is a naturally occurring animal model of CN.

Male and female Gunn rats were injected intravenously (IV) with 3×10¹² or 3×10¹³ genome copies (GC)/kg of AAV8.TBG.hUGT1A1co.WPRE.BGH or vehicle control (phosphate buffered saline [PBS]) at 4 weeks of age. Rats were bled routinely for evaluation of total bilirubin levels. All parameters were compared to vehicle control injected Gunn rats.

Systemic administration of 3×10¹³ GC/kg of AAV8.TBG.hUGT1A1co.WPRE.BGH to Gunn rats reduced hyperbilirubinemia (5.4 mg/dl) to normal levels (0.1-0.3 mg/dl). Thus, the systemic administration of the first generation gene therapy vector for CN attenuated the hyperbilirubinemia characteristic to Gunn rats.

B. Materials and Methods

The purpose of this proof-of-concept (POC) study was to evaluate the first-generation vector designed for the treatment of Crigler-Najjar (CN), AAV8.TBG.hUGT1A1co.WPRE.BGH, with regards to hUGT1A1 expression and total bilirubin levels in Gunn rats. Phosphate buffered saline (PBS) was used as a control. The intravenous (IV) route via the tail vein was selected for use because it is the most efficient route used to target the liver, which in humans is the clinical site of the disease. Efficacy of the test article was determined by total bilirubin levels in serum. In addition, immunohistochemical (IHC) analysis was performed to determine the levels of hUGT1A1 protein expression in the liver. Changes in the serum total bilirubin levels of the animals were analyzed. Rats were anesthetized and blood collected by retro-orbital technique during the in-life phase of the study or by cardiac puncture at necropsy. Blood was collected in labeled serum gel separator brown top tubes, allowed to clot, and then serum was isolated. At the time of necropsy tissues were collected for transgene expression. Liver samples were fixed in 10% neutral buffered formalin (NBF) and processed for determination of transgene expression by IHC.

C. Results—Effect of Test Article on Serum Total Bilirubin Levels

Serum total bilirubin levels were analyzed. Serum total bilirubin levels were plotted as percentage of baseline total bilirubin due to the range in baseline value. Baseline values in females ranged from 3.3-8.1 mg/dl and 3.0-7.2 mg/dl in males. Following IV administration of AAV vector, there was a dose-dependent decrease in total serum bilirubin in both female and male Gunn rats (FIGS. 5A-5B). At day 7 post-vector administration there was an average 90% reduction in total bilirubin in female Gunn rats at a dose of 3×10¹³ GC/kg. At the lower dose of 3×10¹² GC/kg, there was a 70% reduction in total bilirubin in females. In male Gunn rats the effect of the high dose of vector was enhanced with a 93% reduction in total bilirubin. However, at ten-fold lower dose of the test article there was only 39% reduction in serum total bilirubin. Therefore, IV administration of 3×10¹³ GC/kg of AAV8.TBG.hUGT1Alco.WPRE.BGH reduced the hyperbilirubinemia present in the Gunn rats to normal total bilirubin levels.

hUGT1A1 Expression by Immunohistochemistry: Gunn rats administered with the test and control articles were necropsied on days 98-133 post-vector administration and liver collected, fixed in 10% NBF, and processed for IHC staining for UGT1A1. Staining indicates hepatocytes expressing UGT1A1, which was sustained throughout the life of the rat.)

C. Conclusions

Systemic administration of 3×10¹³ GC/kg of AAV8.TBG.hUGT1Alco.WPRE.BGH to Gunn rats reduced hyperbilirubinemia (5.4 mg/dl) to normal levels (0.1-0.3 mg/dl). Thus, the systemic administration of the first generation gene therapy vector for CN attenuated the hyperbilirubinemia characteristic to Gunn rats.

Example 7

Non-Clinical Study Pharmacology/Toxicology Study in Non-Human Primates

A. Summary

The purpose of this study was to evaluate the potential toxicity and tolerability of AAV8.TBG.U201DPmod.BGH (termed AAV8.TBG.hUGT1A1 co) following intravenous (IV) administration in rhesus macaques. For this non-clinical pharmacology/toxicology study, rhesus macaques received an infusion of one of two doses of AAV8.TBG.hUGTlA1co into a peripheral vein. The two doses used for this study were 1.0×10¹³ and 2.5×10¹³ genome copies (GC)/kg. A cohort of animals received infusion of a vehicle only (1× Dulbecco's phosphate buffered saline [DPBS]+0.001% Pluronic® F-68) as a vehicle control.

After vector administration, the animals were monitored daily for general observations. The nonhuman primates (NHPs) were monitored on a weekly basis for comprehensive clinical pathology (cell counts with differentials, clinical chemistries, and coagulation panel) and on a bi-weekly basis for immune reactions to the gene transfer vector (neutralizing antibodies [NAb] to AAV8 capsid, and peripheral cytotoxic T lymphocyte [CTL] responses against both the capsid and transgene assessed by IFN-γ ELISPOT assay).

On day 28 post-vector administration, a mini laparotomy procedure was performed to isolate liver tissue. Liver tissue was evaluated transgene expression by various methods, including by immunohistochemical (IHC) analysis to determine the levels of hUGT1A1 protein expression in the liver.

Animals were sacrificed at day 56 post-test or control article administration. Blood was collected at necropsy for comprehensive clinical pathology and peripheral blood mononuclear cell (PBMC) isolation. Sacrificed animals were necropsied with tissues harvested for a comprehensive histopathological examination. Histopathology slides were evaluated in a blinded manner and peer reviewed. Lymphocytes were harvested from the liver, spleen, and bone marrow to examine the presence of CTLs in these organs at the time of necropsy. Samples of the liver taken at necropsy were also evaluated for transgene expression by various methods, including by IHC analysis to determine the levels of hUGT1A1 protein expression in the liver, and DNA and RNA extraction for genome copy and transgene expression analysis by qPCR and RT-PCR, respectively.

The animals tolerated the infusion of test article well without any apparent long-term or short-term clinical sequelae. Levels of vector GC in the liver were similar to those seen previously with the same capsid (AAV8) in rhesus macaques. Therefore, it was predicted that the target organ for efficacy, which is the liver, would also be the most likely source of toxicity. A detailed review of tissues harvested at necropsy on day 56 post-test or control article administration revealed some minimal to mild findings in liver. The findings in the liver included minimal to mild mononuclear cell infiltrates in the portal region, mild subcapsular fibrosis, minimal to mild bile duct hyperplasia, minimal Ito cell hyperplasia, and one minimal foreign body reaction. Other mild histopathology findings included mononuclear cell infiltrate in the myocardium, lymphoplasmacytic and mononuclear cell infiltrate in the mucosa of the colon, lymphocytic infiltrate in the rectum, lymphoplasmacytic infiltrate in the mucosa of the stomach, and mononuclear cell infiltrate in the trachea. The gastrointestinal findings occurred across the cohorts and were unrelated to dose of the test article. There was one moderate finding of mononuclear cell infiltrate in the epicardium in one animal from the low dose cohort.

Clinical pathology focused on abnormalities in transaminases. Except for one macaque in the high dose of test article group (2.5×10¹³ GC/kg), the elevations in ALT were <6× baseline and <4× baseline for AST (fold-change over baseline levels were determined for each macaque individually). Due to variation between animals in the dosing cohorts, the only statistically significant difference was in AST values between the high dose of test article group vs. the control group when analyzed across all time points using linear mixed-effect modelling. The elevations in ALT or AST levels did not correlate with capsid or transgene T cell responses as while the CTL response in macaques RQ9201 and RA1261 persisted to the end of the study, ALT and AST elevations were trending downwards towards baseline levels by day 56 post-test article administration. Interestingly, the observation of a highly specific T cell response to hUGT1A1 peptide pool A seen in macaque RA1846 occurred in the absence of any deviation of ALT or AST values from baseline levels. This strongly suggests that expression is not affected by the abnormalities in clinical pathology or the appearance of T cells.

As the wild type rhesus macaques used from this study do not demonstrate hyperbilirubinemia it is impossible to determine efficacy of the test article in this model. Therefore, the minimally effective dose (MED) was determined in the mouse model of CN.

Therefore, the key findings from this pharmacology/toxicology study that will inform the design of the clinical trial are:

DLTs were not observed in this toxicology study at the highest dose tested, which was 2.5×10¹³ GC/kg in rhesus macaques. This suggests that the actual MTD is higher than this dose.

The data presented from these studies demonstrate an example of the safety of AAV8.TBG.U201DPmod.BGHfor the treatment of Crigler-Najjar in rhesus macaques.

B. Materials and Methods

AAV8.TBG.U201DPmod.BGH (alternative termed AAV8.TBG.hUGT1A1co) was diluted in sterile 1× Dulbecco's phosphate buffered saline (DPBS)+0.001% Pluronic F-68. Control animals will be injected with vehicle buffer containing no test article. This will serve as the vehicle control for this study. Vehicle control (1× Dulbecco's phosphate buffered saline [DPBS]; pH 7.0-7.3; no calcium, no magnesium, no phenol red)+0.001% Pluronic® F-68) (difunctional block copolymer non-ionic surfactant terminating in primary hydroxyl groups).

Male and female rhesus macaques were used in this study. NHPs assigned to test article groups received either 1.0×10′ genome copies (GC) per kilogram (kg) of body weight or 2.5×10¹³ GC/kg of AAV8.TBG.U201DPmod.BGH in a volume of 10 ml. NHPs assigned to the control article cohort received 10 ml of vehicle control. Test and control articles were administered into a peripheral vein. The intravenous (IV) route via a peripheral vein was selected for use because it is the most efficient route used to target the liver, the clinical site of the disease.

Doses of 1.0×10¹³ GC/kg and 2.5×10¹³ GC/kg AAV8.TBG.U201DPmod.BGH were chosen for this study. The highest dose that we propose to administer in the clinical trial is 1.0×10¹³ GC/kg. Therefore, for this study doses were selected that reflect a dose that is the highest dose of the clinical trial (1.0×10¹³ GC/kg AAV8.TBG.U201DPmod.BGH) and a dose that is 2.5-fold higher than the highest dose planned for the clinical trial (2.5×10¹³ GC/kg AAV8.TBG.U201DPmod.BGH).

Differences in ALT and AST levels compared to baseline levels were analyzed statistically by Wilcoxon rank sum test and overall differences in ALT and AST values across all time points using linear mixed-effect model. Comparisons between two groups were performed using unpaired Student's t-test and comparisons between multiple groups were performed using one-way analysis of variance (ANOVA, Tukey's Multiple Comparison post-test). All values expressed as mean±standard error of the mean (SEM) unless otherwise stated. Ranges of normal values for wild type rhesus macaques were generated by taking the mean of all values collected for the study animals pre-vector administration and by calculating the standard deviation (SD). The range will be presented as the mean±SD. Values outside of two SDs of the mean will be considered to be extreme values. A p value of <0.05 was considered significant.

C. Results

All rhesus macaques survived until their scheduled necropsy time point at day 56 post-test or control article administration. All rhesus macaques were visually examined each time that they were anesthetized. All changes or abnormalities were noted in the study file. There were no abnormalities noted during the course of the study. Throughout the study, the body weight of the animals was monitored at each time point listed in the study protocol. All animals either maintained their weight or continued to gradually gain weight over the course of the study.

Liver function tests (LFTs) focusing on alkaline phosphatase (ALT) and aspartate aminotransferase (AST) levels were monitored. Other parameters reflective of liver pathology, such as total bilirubin, were within normal limits throughout.

Ranges of normal values for the rhesus macaques were generated by taking the mean of all values collected for the study animals pre-vector administration and by calculating the standard deviation (SD).

$\frac{{ALT}\left( {U/1} \right)}{44 \pm 27}\mspace{20mu}\frac{{AST}\left( {U/1} \right)}{29 \pm 6}$

Prior to vector administration there was some variation in the baseline levels of ALT across the animals in the study, ranging from 17 U/l at day −16 for RA1260 to 110 U/l at day −7 for RA1261. ALT and AST values post-vector administration were evaluated for significant changes compared to the average baseline values (mean of days −16, −7, and 0 prior to vector administration). Differences in ALT and AST levels compared to baseline levels were analyzed statistically by Wilcoxon rank sum test. Due to the variation between animals administered with the same dose of test article, there were no significant differences between any study day post-test or control article administration. In addition, overall differences in ALT and AST values across all time points were analyzed using linear mixed-effect modelling. Again, due to the variation between animals administered with the same dose of test article, there was no significant difference in ALT values for the high dose of test article group (2.5×10¹³ GC/kg) vs. the control group (p value=0.142) and for the low dose of test article group (2.5×10¹³ GC/kg) vs. the control group (p value=0.564) or in AST values for the low dose of test article group vs. the control group (p value=0.255). There was a statistically significant difference in AST values from the high dose of test article vs. the control group (p value=0.010).

Prior to initiation of the study, all rhesus macaques were screened for neutralizing antibodies (NAbs) to AAV8 capsid by the Immunology Core at GTP. All 8 animals selected for the study were seronegative (NAb titer<1:5). Following test article administration, all animals developed an AAV8-specific NAb response. On day 8 post-vector, AAV8 NAb titers increased from <1:5 to 1:40-1:1280. There was no dose-dependent effect of test article on NAb titer as there was a similar and overlapping spread of NAb titers at day 8 following administration of either 1.0×10¹³ GC/kg or 2.5×10¹³ GC/kg of test article. Following day 8 post-vector administration, AAV8 NAb titers did gradually decrease at days 14 and 21 post-vector administration. Interestingly, the NAb response increased at days 28 and 35 post-vector administration and remained at similar levels until the end of the study. Control article injected animals remained seronegative or had titers of 1:5 throughout the study. Natural fluctuations in AAV8 NAb titers in non-injected animals have been described before (Calcedo et al., 2016 Hum. Gene Ther. Clin. Dev.).

RNA was extracted from liver samples. Animals administered the high dose of test article had on average higher levels of vector GC in the liver (FIG. 6A and 6B). Following comparison of the average corrected relative expression in the liver across the test article dose groups there was no significant difference between the test article administered groups (Student's t test, p=0.408).

D. Summary

Rhesus macaques received an infusion of one of two doses of AAV8.TBG.U201DPmod.BGH (AAV8 capsid with genome of SEQ ID NO: 15, i.e., AAVS′ and 3′ ITRs, two copies of alpha mic/bik enhancer, TBG promoter, hUGT1A1 of SEQ ID NO: 12, BGH polyA) into a peripheral vein. The two doses used for this study were 1.0×10¹³ and 2.5×10¹³ GC/kg. An additional cohort of animals received control article as a vehicle control. Blood was collected at the indicated time points for comprehensive clinical pathology. Animals were necropsied on day 56 post-test or control article administration with tissues harvested for comprehensive histopathological examination. Additional evaluations during both the in-life phase of the study and at necropsy included analysis of anti-AAV8 NAbs, AAV8 capsid-specific and hUGT1A1-specific peripheral CTL responses, CTL responses in the liver, spleen, and bone marrow, IHC for hUGT1A1 expression in liver, and determination of vector GC and transgene mRNA expression.

The animals tolerated the infusion of test article well without any apparent long-term or short-term clinical sequelae. Levels of vector GC in the liver were similar to those seen previously with the same capsid (AAV8) in rhesus macaques. Therefore, it was predicted that the target organ for efficacy, which is the liver, would also be the most likely source of toxicity. A detailed review of tissues harvested at necropsy on day 56 post-test or control article administration revealed some minimal to mild findings in liver. The findings in the liver included minimal to mild mononuclear cell infiltrates in the portal region, mild subcapsular fibrosis, minimal to mild bile duct hyperplasia, minimal Ito cell hyperplasia, and one minimal foreign body reaction. Other mild histopathology findings included mononuclear cell infiltrate in the myocardium, lymphoplasmacytic and mononuclear cell infiltrate in the mucosa of the colon, lymphocytic infiltrate in the rectum, lymphoplasmacytic infiltrate in the mucosa of the stomach, and mononuclear cell infiltrate in the trachea. The gastrointestinal findings occurred across the cohorts and were unrelated to dose of the test article. There was one moderate finding of mononuclear cell infiltrate in the epicardium in one animal from the low dose cohort.

Clinical pathology focused on abnormalities in transaminases. Except for one macaque in the high dose of test article group (2.5×10¹³ GC/kg), the elevations in ALT were <6× baseline and <4× baseline for AST (fold-change over baseline levels were determined for each macaque individually). Due to variation between animals in the dosing cohorts, the only statistically significant difference was in AST values between the high dose of test article group vs. the control group when analyzed across all time points using linear mixed-effect modelling. The elevations in ALT or AST levels did not correlate with capsid or transgene T cell responses as while the CTL response in macaques RQ9201 and RA1261 persisted to the end of the study, ALT and AST elevations were trending downwards towards baseline levels by day 56 post-test article administration. Interestingly, the observation of a highly specific T cell response to hUGT1A1 peptide pool A seen in macaque RA1846 occurred in the absence of any deviation of ALT or AST values from baseline levels. This strongly suggests that expression is not affected by the abnormalities in clinical pathology or the appearance of T cells.

As the wild type rhesus macaques used from this study do not demonstrate hyperbilirubinemia it is impossible to determine efficacy of the test article in this model. Therefore, the minimally effective dose (MED) was determined in the mouse model of CN.

There were no dose limiting toxicities observed, meaning that the maximally tolerated dose is equal to or greater than 2.5×10¹³ GC/kg.

Example 8 Non-Clinical Efficacy Study of AAV8.TBG.hUGT1A1co. BGH in the UGT1 Knockout Mouse

A. Summary

The purpose of this study was to determine the minimally effective dose (MED) in the CN mouse model, the UGT 1 knockout (KO) mouse. UGT1 KO mice received an intravenous (IV) injection via the tail vein of one of four doses of the vector, AAV8.TBG.U201mod.BGH (termed AAV8.TBG.hUGT1A1co in the figure and figure legend). The doses used for this study were 2.5×10¹⁰, 2.5×10¹¹, 2.5×10¹², and 2.5×10¹³ genome copies (GC)/kg. A cohort of animals received vehicle only (1× Dulbecco's phosphate buffered saline [DPBS]+0.001% Pluronic F-68) as a vehicle control.

Group dosing dates were staggered based on availability of UGT1 KO mice. At the initiation of the study, available mice within the dosing age range were randomly assigned to first the high dose vector group (2.5×10¹³ GC/kg) and the vehicle control group. Subsequently, mice were assigned to vector dose groups in the following order: 2.5×10¹², 2.5×10¹⁰, and 2.5×10¹¹ GC/kg. After vector administration, the animals were monitored daily for general observations. Blood was collected from animals at the indicated time points to capture serum total bilirubin levels.

Animals were sacrificed on day 56 post-test or control article administration. Blood was collected at necropsy for a serum chemistry panel and hematology panel. Sacrificed animals were necropsied and tissues harvested for a comprehensive histopathological examination. Histopathology slides were evaluated in a blinded manner and peer reviewed. Where findings were observed at the highest vector dose, the same tissue at the subsequent lower vector doses was evaluated until no findings exist, or all dose groups were evaluated.

Efficacy of the test article was determined by total bilirubin levels in serum. In addition, Western blot and immunohistochemical (IHC) analysis were performed to determine the levels of hUGT1A1 protein expression in the liver.

There were no apparent clinical sequelae in any groups and abnormalities in clinical pathology were restricted to elevations in the liver transaminases ALT and AST ranged from 1-9.1× baseline for ALT and were primarily found in male mice at day 28 post-vector administration of the highest dose of the test article. The abnormalities were dose-dependent and there were essentially no findings in animals that received lower doses of the test article. While there were histopathological findings in male mice administered with the control article, the majority of the findings were in male mice administered with the highest dose of the test article (2.5×10¹³ GC/kg) but all findings were minimal to mild. Therefore, it was concluded that there were no dose limiting toxicities seen, meaning that the maximally tolerated dose was greater than or equal to the highest dose tested, which was 2.5×10¹³ GC/kg. The presence of increased liver pathology (minimal to mild) at this dose, suggested it is related to the test article, indicating that the no effect dose is the next lower dose of 2.5×10¹² GC/kg.

The conduct of this study in the animal model of CN allowed the MED to be estimated. At doses of the test article greater than 2.5×10¹⁰ GC/kg, there was a complete reversal of total bilirubin levels to baseline levels of 0.1-0.3 mg/dl. Administration of 2.5×10¹⁰ GC/kg resulted in a 79% reduction in serum total bilirubin levels in male mice at day 14 post-vector administration, which gradually increased to a 57% reduction at day 28, and returned to baseline hyperbilirubinemia by day 42 and administration of the same dose in a single female UGT1 KO mouse did not result in a deviation from baseline values. While there was a sex difference with respect to expression of hUGT1A1 in UGT1 KO mice, this has not been seen to translate to nonhuman primates. Therefore, the MED is equal to 2.5×10¹¹ GC/kg.

B. Methods

AAV8.TBG.U201DPmod.BGH was diluted in sterile 1× Dulbecco's phosphate buffered saline (DPBS)+0.001% Pluronic F-68. Vehicle control (1× Dulbecco's phosphate buffered saline [DPBS]+0.001% Pluronic F-68)

Male and female UGT1 KO mice (n=50, 25 male and 25 female) 6 to 20 weeks in age were used in this study and necropsied at day 56 post-vector administration. Animals were ear tagged and assigned to one of five cohorts.

The IV route via the tail vein was selected for use because it is the most efficient route used to target the liver, which in humans is the clinical site of the disease.

Multiple dose levels of AAV8.TBG.U201DPmod.BGH were examined. The highest dose was 2.5×10¹³ GC/kg, which is 2.5-fold higher than the highest dose of a proposed clinical trial. The doses selected differed by one log and were 2.5×10¹⁰ GC/kg, 2.5×10¹¹ GC/kg, 2.5×10¹² GC/kg, and 2.5×10¹³ GC/kg. Each group included 5 animals of each sex. Five animals per group is the minimal number to enable statistical analysis of study outcome.

Efficacy of the test article was determined by total bilirubin levels in serum. In addition, Western blot and immunohistochemical (IHC) analysis were performed to determine the levels of hUGT1A1 protein expression in the liver.

For body weight, food consumption, ALT, AST, total bilirubin, Western blot quantification, vector GC, and hUGT1A1 mRNA transcript data, cohort average and standard error of the mean (SEM) was calculated and reported. Differences in ALT, AST and total bilirubin levels compared to baseline levels were analyzed statistically by Wilcoxon rank sum test and overall differences in ALT, AST, and total bilirubin values across all time points using linear mixed-effect model. Comparisons between two groups were performed using unpaired Student's t-test and comparisons between multiple groups were performed using one-way analysis of variance (ANOVA, Tukey's Multiple Comparison post-test). All values expressed as mean±SEM unless otherwise stated. A p value of <0.05 was considered significant.

C. Results

During the course of the study mouse ID 5205 was euthanized on day 8 post-vector administration for clinical signs (displayed moribund condition thus requiring euthanasia for humane reasons). A full necropsy was performed and tissues were collected. Following test or control article administration, animals were monitored daily for general observations. All changes or abnormalities were noted in the study file. With the exception of mouse ID 5205 that was euthanized prior to the necropsy time point, there were observations recorded for 10 out of the 41 mice enrolled on the study that did not affect study outcome. Seven of these 10 mice required treatment with supportive care during the in-life phase of the study.

Blood chemistry results were evaluated for statistical change (p<0.05) compared to mice administered with the control article (100 μl of vehicle control) at each time point. Of interest were three distinct parameters; total bilirubin, ALT, and AST as there were consistent substantial differences between groups.

The abnormalities in liver function tests (LFTs) increased with the increasing dose of the test article and elevations greater than 4× baseline (colored orange and red) were restricted to the highest dose group (2.5×10¹³ GC/kg), with the exception of one male mouse in the lowest dose group (2.5×10¹⁰ GC/kg) at day 14 and one male mouse that received a dose of 2.5×10¹¹ GC/kg at day 28 post-test article administration. Elevations of AST gave a similar pattern but the elevations were limited to <4× baseline (colored green and blue), with the exception of one female mouse that received a dose of 2.5×10¹² GC/kg at day 56 post-test article administration.

Comparison of ALT and AST levels across the cohorts was performed using linear mixed effect modelling and stratified by sex. For ALT, there was a significant elevation compared to the control group observed in both male and female mice administered with the highest dose of the test article, 2.5×10¹³ GC/kg (p=0.015 for males, p=0.049 for females). A significant elevation in AST was only observed in female mice administered with the highest test article dose compared to the control group (p=0.042).

Total bilirubin levels in UGT1 KO mice injected with the control article (vehicle control) were similar across all time points with no variation in levels between males and females (FIG. 6). As expected we observed a rapid and significant reduction of total bilirubin by day 14 post-vector administration in both male and female mice treated at all doses of the test article (2.5×10¹⁰ GC/kg, 2.5×10¹¹ GC/kg, 2.5×10¹² GC/kg, and 2.5×10¹³ GC/kg of AAV8.TBG.U201DPmod.BGH). At doses of the test article greater than 2.5×10¹⁰ GC/kg, there was a complete reversal of total bilirubin levels to baseline levels of 0.1-0.3 mg/dl (FIG. 7). Administration of 2.5×10¹⁰ GC/kg resulted in a 79% reduction in serum total bilirubin levels in male mice at day 14 post-vector administration, which gradually increased to a 57% reduction at day 28, and returned to baseline hyperbilirubinemia by day 42 (FIG. 7). Administration of the same dose in a single female UGT1 KO mouse did not result in a deviation from baseline values.

Comparison of total bilirubin levels across the cohorts was performed using linear mixed effect modelling and stratified by sex. A significant reduction in total bilirubin compared to the control group was observed in males for all dose groups and for female mice dosed with 2.5×10¹² GC/kg and 2.5×10¹³ GC/kg (p<0.05).

At the time of necropsy, liver was harvested for determination of hUGT1A1 transgene expression. Liver samples were snap frozen and stored at −80° C. prior to use. Expression was evaluated by detection of hUGT1A1 protein levels by Western blot on liver homogenates. Human UGT1A1-specific antibodies were used for detection and Western blot images were quantified against the same amount of protein from a positive control sample. Expression of hUGT1A1 in male mice increased significantly with dose of the test article from 2.5×10¹² GC/kg to 2.5×10¹³ GC/kg (p<0.05, FIG. 8). Bands for male mice injected with 2.5×10¹¹ GC/kg were below the limit of detection.

RNA was extracted from liver samples. TaqMan qPCR reactions were performed. Expression of hUGT1A1 mRNA transcript in the liver of male mice did not significantly differ with dose of the test article from 2.5×10¹² GC/kg to 2.5×10¹³ GC/kg (FIGS. 9A-9B).

D. Summary of Results

Male and female UGT1 KO mice 6-20 weeks of age were administered IV with one of four doses [2.5×10¹⁰, 2.5×10¹¹, 2.5×10¹², and 2.5×10¹³ GC/kg] of AAV8.TBG.U201DPmod.BGH. The doses chosen were to reflect the span of the proposed dosing regimen of the clinical trial. An additional cohort of animals received control article as a vehicle control. Blood was collected from animals at the indicated time points to capture total bilirubin levels. Animals were necropsied on day 56 post-test or control article administration with tissues harvested for comprehensive histopathological examination. Additionally, blood was collected for serum chemistry panel and hematology panel.

A number of factors were considered in the design of this study. First, we selected to conduct the experiments in UGT1 KO mice (rather than in C57BL/6J mice) for two reasons. First, using this strain of mice would allow us to evaluate efficacy in parallel with toxicity. Second, we wanted to evaluate vector-associated toxicity in the setting of any pathology associated with the defect in UGT1A1, and the associated hyperbilirubinemia and its sequelae. While we did not expect there to be liver pathology in the model, we were concerned that some level of chronic severe hyperbilirubinemia could influence the response of the host liver to vector.

The key findings are as follows:

-   -   No clinical sequelae     -   Efficacy         -   At doses of the test article greater than 2.5×10¹⁰ GC/kg,             there was a complete reversal of total bilirubin levels to             baseline levels of 0.1-0.3 mg/dl.         -   A significant reduction in total bilirubin compared to the             control group was observed in males for all four dose groups             (2.5×10¹⁰-2.5×10¹³ GC/kg) and for female mice dosed with             2.5×10¹² GC/kg and 2.5×10¹³ GC/kg (p<0.05).         -   Administration of 2.5×10¹⁰ GC/kg resulted in a 79% reduction             in serum total bilirubin levels in male mice at day 14             post-vector administration, which gradually increased to a             57% reduction at day 28, and returned to baseline             hyperbilirubinemia by day 42.         -   Administration of the same dose in a single female UGT1 KO             mouse did not result in a deviation from baseline values.         -   The sex difference seen in expression in mice has not been             seen to translate to nonhuman primates. Therefore, the MED             is equal to 2.5×10¹¹ GC/kg.     -   Clinical Pathology         -   Transaminases: Abnormalities were limited to elevations of             the liver function tests ALT and AST that ranged from 1-9.1×             baseline for ALT and were primarily found in male mice at             day 28 post-vector administration of the highest doses of             test article. The abnormalities were dose-dependent and             there were essentially no findings in animals that received             lower doses of the test article. Therefore, we conclude that             the no effect dose based on these criteria is 2.5×10¹²             GC/kg.     -   Pathology: There were three gross observations, none of which         involved the liver (the target organ for this gene therapy         approach). Histopathology was limited to minimal or mild         findings in liver as follows:         -   Control article administered male and female mice had no             abnormalities detected, with the exception of minimal             findings of centrilobular single cell hepatocellular             necrosis/degeneration and intracanalicular bile stasis in             one male mouse.         -   Overall, there were fewer findings in the liver of female             mice. Only minimal findings were observed of centrilobular             single cell hepatocellular necrosis/degeneration and             mononuclear cell infiltration in one mouse administered with             the high dose of the test article (2.5×10¹³ GC/kg) and one             mouse administered with 2.5×10¹² GC/kg. In addition, the             female mouse administered with 2.5×10¹² GC/kg also had             hepatocellular mitotic figures and bile stasis.         -   Minimal centrilobular single cell hepatocellular             necrosis/degeneration was seen in all cohorts of male UGT1             KO mice. However, in the high dose of test article cohort             (2.5×10¹³ GC/kg) there were also two mild findings of             centrilobular single cell hepatocellular             necrosis/degeneration. This cohort also displayed minimal             findings of mononuclear cell infiltration, hepatocellular             mitotic figures and bile stasis.         -   Tissues other than the liver were only reviewed for the high             dose test article (2.5×10¹³ GC/kg) and control article             administered mice. The only other observations were findings             in the lung (minimal and mild accumulation of acidophilic             material in alveolar macrophages in male and female mice             administered with the control article), uterus (minimal             focal subacute inflammation in one female mouse administered             with the control article), and skin of the injection site             (dermal fibrosis in one female mouse administered with the             high dose of the test article).

There were no dose limiting toxicities seen, meaning that the maximally tolerated dose was greater than or equal to the highest dose tested, which was 2.5×10¹³ GC/kg

Based on mild findings in liver pathology at the highest dose (2.5×10¹³ GC/kg), we propose the no effect dose to be next lower dose of 2.5×10¹² GC/kg

The MED is equal to 2.5×10¹¹ GC/kg.

(Sequence Listing Free Text)

The following information is provided for sequences containing free text under numeric identifier <223>.

SEQ ID NO: (containing free text) Free text under <223>  1 <223> Engineered UGT1A1 sequence U001 2 <223> Engineered UGT1A1 sequence U011TY 3 <223> Engineered UGT1A1 sequence U201DP 4 <223> Engineered UGT1A1 sequence 7 <223> optimized UGT1A1 v2.1 8 <223> optimized UGT1A1 v3 9 <223>  pAAV.TBG.hUGT1A1co.WRPE.BGH (p3793) vector <220> <221> repeat_region <222> (1) . . . (168) <223> 5′ ITR <220> <221> enhancer <222> (211) . . . (310) <223> alpha mic/bik <220> <221> enhancer <222> (317) . . . (416) <223> alpha mic/bik <220> <221> promoter <222> (431) . . . (907) <223> TBG promoter <220> <221> Intron <222> (939) . . . (1071) <223> SV40 misc intron (Promega) <220> <221> misc_feature <222> (1086) . . . (1091) <223> Kozak <220> <221> misc_feature <222> (1092) . . . (2690) <223> UGT1A1 CDS <220> <221> misc_feature <222> (2709) . . . (3250) <220> <221> polyA_signal <222> (3257) . . . (3471) <223> BGH polyA <220> <221> repeat_region <222> (3521) . . . (3558) <223> 3′ ITR <220> <221> misc_feature <222> (4451) . . . (5308) <223> Amp-R CDS <220> <221> misc_feature <222> (5482) . . . (6070) <223> origin 10 <223>  pAAV.TBG.hUGT1A1co.BGH <220> <221> repeat_region <222> (1) . . . (168) <223> 5′ ITR <220> <221> enhancer <222> (211) . . . (310) <223> alpha mc/bik <220> <221> enhancer <222> (317) . . . (416) <223> alpha mc/bik <220> <221> promoter <222> (431) . . . (907) <223> TBG promoter <220> <221> Intron <222> (939) . . . (1071) <223> SV40 misc intron (Promega) <220> <221> misc_feature <222> (1086) . . . (1091) <223> Kozak <220> <221> misc_feature <222> (1092) . . . (2690) <223> UGT1A1 coding sequence <220> <221> repeat_region <222> (2695) . . . (3152) <223> 3′ ITR <220> <221> polyA_signal <222> (2721) . . . (2935) <223> BGH polyA <220> <221> misc_feature <222> (3915) . . . (4772) <223> Amp-R coding sequence <220> <221> misc_feature <222> (4946) . . . (4772) <223> origin 11 <223> AAV8 VP1 capsid protein 12 <223> engineered UGT1A1 U201DPmod 13 <223> engineered UGT1A1 U001mod 14 <223> engineered UGT1A1 U011TYmod 15 <223> pAAV.TGB.U201DP.BGH (p4120) <220> <221> repeat_region <222> (1) . . . (168) <223> 5′ ITR <220> <221> enhancer <222> (211) . . . (310) <223> alpha mic/bik enhancer <220> <221> enhancer <222> (317) . . . (416) <223> alpha mic/bik enhancer <220> <221> promoter <222> (431) . . . (907) <223> TBG promoter <220> <221> Intron <222> (939) . . . (1071) <223> SV40 misc intron (Promega) <220> <221> misc_feature <222> (1092) . . . (2690) <223> U201DPmod CDS <220> <221> polyA_signal <222> (2709) . . . (2923) <223> BGH polyA <220> <221> repeat_region <222> (2973) . . . (3140) <223> AAV 3′ ITR 16 <223> pAAV.TBG.U011TY.BGH (p4119) <220> <221> repeat_region <222> (1) . . . (168) <223> AAV 5′ ITR <220> <221> enhancer <222> (211) . . . (310) <223> alpha mic/bik <220> <221> enhancer <222> (317) . . . (416) <223> alpha mic/bik <220> <221> promoter <222> (431) . . . (907) <223> TBG promoter <220> <221> Intron <222> (939) . . . (1071) <223> SV40 misc intron (Promega) <220> <221> misc_feature <222> (1092) . . . (2690) <223> CDS for modfied U011TY <220> <221> polyA <222> (2709) . . . (2923) <223> BGH polyA <220> <221> repeat_region <222> (2973) . . . (3140) <223> AAV 3′ITR 17 <223> pAAV.TBG.U001.BGH (p4118) 18 <223> engineered UG1A1 U3G

All publications, patents, patent applications, cited in this application and the Sequence Listing referenced herein, as well as U.S. Provisional Patent Application Nos. 62/348,029, filed Jun. 9, 2016, and No. 62/266,969, filed Dec. 14, 2015, are hereby incorporated by reference in their entireties as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference. Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications can be made thereto without departing from the spirit or scope of the appended claims. 

1. An adeno-associated virus (AAV) vector comprising an AAV capsid and a vector genome comprising a UGT1A1 coding sequence operably linked to expression control sequences which direct transcription and/or expression of human UGT1A1, wherein the UGT1A1 coding sequence is: (a) SEQ ID NO: 12; (b) SEQ ID NO: 13; (c) SEQ ID NO: 14; (d) SEQ ID NO: 3; (e) SEQ ID NO: 2; or (f) SEQ ID NO: 1; or a sequence at least 99% identical to SEQ ID NO: 12, 13, 14, 3, 2, or 1 that encodes human UGT1A1. 